diff --git a/README.md b/README.md
index 25a59f9..15482e6 100755
--- a/README.md
+++ b/README.md
@@ -34,6 +34,7 @@ Some days later, update the repository:
 genome_updater downloads and keeps several snapshots of a certain sub-set of the genomes repository, without redundancy and with incremental track of changes.
 
 - it runs on a working directory (defined with `-o`) and creates a snapshot (optionally named with `-b`, timestamp by default) of refseq and/or genbank (`-d`) genome repositories based on selected organism groups (`-g`) and/or taxonomic ids (`-T`) with the desired files type(s) (`-f`)
+- files are downloaded to a single folder by default ("{prefix}files/") but can be also saved in the NCBI ftp file structure (`-N`)
 - filters can be applied to refine the selection: refseq category (`-c`), assembly level (`-l`), dates (`-D`/`-E`), custom filters (`-F`), [top assemblies](#Top-assemblies) (`-A`)
 - `-M gtdb` enables GTDB [3] compability. Only assemblies from the latest GTDB release will be kept and taxonomic filters will work based on GTDB nodes (e.g. `-T "c__Hydrothermarchaeia"` or `-A genus:3`)
 - the repository can be updated or changed with incremental changes. outdated files are kept in their respective version and repeated files linked to the new version. genome_updater keepts track of all changes and just downloads what is necessary
@@ -49,7 +50,7 @@ or direct file download:
 	wget https://raw.githubusercontent.com/pirovc/genome_updater/master/genome_updater.sh
 	chmod +x genome_updater.sh
 
- - genome_updater is portable and depends on the GNU Core Utilities + few additional tools (`awk` `bc` `find` `join` `md5sum` `parallel` `sed` `tar` `xargs` `wget`/`curl`) which are commonly available and installed in most distributions. If you are not sure if you have them all, just run `genome_updater.sh` and it will tell you if something is missing (otherwise the it will show the help page).
+ - genome_updater is portable and depends on the GNU Core Utilities + few additional tools (`awk` `bc` `find` `join` `md5sum` `parallel` `sed` `tar` `wget`/`curl`) which are commonly available and installed in most distributions. If you are not sure if you have them all, just run `genome_updater.sh` and it will tell you if something is missing (otherwise the it will show the help page).
 
 To test if all genome_updater functions are running properly on your system:
 
@@ -197,96 +198,99 @@ or
 
 ## Parameters
 
-	┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐    ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐
-	│ ┬├┤ ││││ ││││├┤     │ │├─┘ ││├─┤ │ ├┤ ├┬┘
-	└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴  ─┴┘┴ ┴ ┴ └─┘┴└─
-	                                     v0.5.1 
-
-	Database options:
-	 -d Database (comma-separated entries)
-		[genbank, refseq]
-
-	Organism options:
-	 -g Organism group(s) (comma-separated entries, empty for all)
-		[archaea, bacteria, fungi, human, invertebrate, metagenomes, 
-		other, plant, protozoa, vertebrate_mammalian, vertebrate_other, viral]
-		Default: ""
-	 -T Taxonomic identifier(s) (comma-separated entries, empty for all).
-		Example: "562" (for -M ncbi) or "s__Escherichia coli" (for -M gtdb)
-		Default: ""
-
-	File options:
-	 -f file type(s) (comma-separated entries)
-		[genomic.fna.gz, assembly_report.txt, protein.faa.gz, genomic.gbff.gz]
-		More formats at https://ftp.ncbi.nlm.nih.gov/genomes/all/README.txt
-		Default: assembly_report.txt
-
-	Filter options:
-	 -c refseq category (comma-separated entries, empty for all)
-		[reference genome, representative genome, na]
-		Default: ""
-	 -l assembly level (comma-separated entries, empty for all)
-		[complete genome, chromosome, scaffold, contig]
-		Default: ""
-	 -D Start date (>=), based on the sequence release date. Format YYYYMMDD.
-		Default: ""
-	 -E End date (<=), based on the sequence release date. Format YYYYMMDD.
-		Default: ""
-	 -F custom filter for the assembly summary in the format colA:val1|colB:valX,valY (case insensitive).
-		Example: -F "2:PRJNA12377,PRJNA670754|14:Partial" (AND between cols, OR between values)
-		Column info at https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt
-		Default: ""
-
-	Taxonomy options:
-	 -M Taxonomy. gtdb keeps only assemblies in GTDB (R207). ncbi keeps only latest assemblies (version_status). 
-		[ncbi, gtdb]
-		Default: "ncbi"
-	 -A Keep a limited number of assemblies for each selected taxa (leaf nodes). 0 for all. 
-		Selection by ranks are also supported with rank:number (e.g genus:3)
-		[species, genus, family, order, class, phylum, kingdom, superkingdom]
-		Selection order based on: RefSeq Category, Assembly level, Relation to type material, Date.
-		Default: 0
-	 -a Keep the current version of the taxonomy database in the output folder
-
-	Run options:
-	 -o Output/Working directory 
-		Default: ./tmp.XXXXXXXXXX
-	 -t Threads to parallelize download and some file operations
-		Default: 1
-	 -k Dry-run mode. No sequence data is downloaded or updated - just checks for available sequences and changes
-	 -i Fix only mode. Re-downloads incomplete or failed data from a previous run. Can also be used to change files (-f).
-	 -m Check MD5 of downloaded files
-
-	Report options:
-	 -u Updated assembly accessions report
-		(Added/Removed, assembly accession, url)
-	 -r Updated sequence accessions report
-		(Added/Removed, assembly accession, genbank accession, refseq accession, sequence length, taxid)
-		Only available when file format assembly_report.txt is selected and successfully downloaded
-	 -p Reports URLs successfuly downloaded and failed (url_failed.txt url_downloaded.txt)
-
-	Misc. options:
-	 -b Version label
-		Default: current timestamp (YYYY-MM-DD_HH-MM-SS)
-	 -e External "assembly_summary.txt" file to recover data from. Mutually exclusive with -d / -g 
-		Default: ""
-	 -B Alternative version label to use as the current version. Mutually exclusive with -i.
-		Can be used to rollback to an older version or to create multiple branches from a base version.
-		Default: ""
-	 -R Number of attempts to retry to download files in batches 
-		Default: 3
-	 -n Conditional exit status based on number of failures accepted, otherwise will Exit Code = 1.
-		Example: -n 10 will exit code 1 if 10 or more files failed to download
-		[integer for file number, float for percentage, 0 = off]
-		Default: 0
-	 -L Downloader
-		[wget, curl]
-		Default: wget
-	 -x Allow the deletion of regular extra files (not symbolic links) found in the output folder
-	 -s Silent output
-	 -w Silent output with download progress only
-	 -V Verbose log
-	 -Z Print debug information and run in debug mode
+```
+┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐    ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐
+│ ┬├┤ ││││ ││││├┤     │ │├─┘ ││├─┤ │ ├┤ ├┬┘
+└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴  ─┴┘┴ ┴ ┴ └─┘┴└─
+                                     v0.6.0 
+
+Database options:
+ -d Database (comma-separated entries)
+	[genbank, refseq]
+
+Organism options:
+ -g Organism group(s) (comma-separated entries, empty for all)
+	[archaea, bacteria, fungi, human, invertebrate, metagenomes, 
+	other, plant, protozoa, vertebrate_mammalian, vertebrate_other, viral]
+	Default: ""
+ -T Taxonomic identifier(s) (comma-separated entries, empty for all).
+	Example: "562" (for -M ncbi) or "s__Escherichia coli" (for -M gtdb)
+	Default: ""
+
+File options:
+ -f file type(s) (comma-separated entries)
+	[genomic.fna.gz, assembly_report.txt, protein.faa.gz, genomic.gbff.gz]
+	More formats at https://ftp.ncbi.nlm.nih.gov/genomes/all/README.txt
+	Default: assembly_report.txt
+
+Filter options:
+ -c refseq category (comma-separated entries, empty for all)
+	[reference genome, representative genome, na]
+	Default: ""
+ -l assembly level (comma-separated entries, empty for all)
+	[complete genome, chromosome, scaffold, contig]
+	Default: ""
+ -D Start date (>=), based on the sequence release date. Format YYYYMMDD.
+	Default: ""
+ -E End date (<=), based on the sequence release date. Format YYYYMMDD.
+	Default: ""
+ -F custom filter for the assembly summary in the format colA:val1|colB:valX,valY (case insensitive).
+	Example: -F "2:PRJNA12377,PRJNA670754|14:Partial" (AND between cols, OR between values)
+	Column info at https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt
+	Default: ""
+
+Taxonomy options:
+ -M Taxonomy. gtdb keeps only assemblies in GTDB (R207). ncbi keeps only latest assemblies (version_status). 
+	[ncbi, gtdb]
+	Default: "ncbi"
+ -A Keep a limited number of assemblies for each selected taxa (leaf nodes). 0 for all. 
+	Selection by ranks are also supported with rank:number (e.g genus:3)
+	[species, genus, family, order, class, phylum, kingdom, superkingdom]
+	Selection order based on: RefSeq Category, Assembly level, Relation to type material, Date.
+	Default: 0
+ -a Keep the current version of the taxonomy database in the output folder
+
+Run options:
+ -o Output/Working directory 
+	Default: ./tmp.XXXXXXXXXX
+ -t Threads to parallelize download and some file operations
+	Default: 1
+ -k Dry-run mode. No sequence data is downloaded or updated - just checks for available sequences and changes
+ -i Fix only mode. Re-downloads incomplete or failed data from a previous run. Can also be used to change files (-f).
+ -m Check MD5 of downloaded files
+
+Report options:
+ -u Updated assembly accessions report
+	(Added/Removed, assembly accession, url)
+ -r Updated sequence accessions report
+	(Added/Removed, assembly accession, genbank accession, refseq accession, sequence length, taxid)
+	Only available when file format assembly_report.txt is selected and successfully downloaded
+ -p Reports URLs successfuly downloaded and failed (url_failed.txt url_downloaded.txt)
+
+Misc. options:
+ -b Version label
+	Default: current timestamp (YYYY-MM-DD_HH-MM-SS)
+ -e External "assembly_summary.txt" file to recover data from. Mutually exclusive with -d / -g 
+	Default: ""
+ -B Alternative version label to use as the current version. Mutually exclusive with -i.
+	Can be used to rollback to an older version or to create multiple branches from a base version.
+	Default: ""
+ -R Number of attempts to retry to download files in batches 
+	Default: 3
+ -n Conditional exit status based on number of failures accepted, otherwise will Exit Code = 1.
+	Example: -n 10 will exit code 1 if 10 or more files failed to download
+	[integer for file number, float for percentage, 0 = off]
+	Default: 0
+ -N Output files in folders like NCBI ftp structure (e.g. files/GCF/000/499/605/GCF_000499605.1_EMW001_assembly_report.txt)
+ -L Downloader
+	[wget, curl]
+	Default: wget
+ -x Allow the deletion of regular extra files (not symbolic links) found in the output folder
+ -s Silent output
+ -w Silent output with download progress only
+ -V Verbose log
+ -Z Print debug information and run in debug mode
+```
 
 ## References:
 
diff --git a/genome_updater.sh b/genome_updater.sh
index 992cee1..a27ae33 100755
--- a/genome_updater.sh
+++ b/genome_updater.sh
@@ -25,7 +25,7 @@ IFS=$' '
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
-version="0.5.2"
+version="0.6.0"
 
 # Define ncbi_base_url or use local files (for testing)
 local_dir=${local_dir:-}
@@ -91,6 +91,42 @@ download_retry_md5(){ # parameter: ${1} url, ${2} output file, ${3} url MD5, ${4
     return 1; # failed to check md5 after all attempts
 }
 
+path_output() # parameter: ${1} file/url
+{
+    f=$(basename ${1});
+    path="${files_dir}";
+    if [[ "${ncbi_folders}" -eq 1 ]]; then
+        path="${path}${f:0:3}/${f:4:3}/${f:7:3}/${f:10:3}/";
+    fi
+    echo "${path}";
+}
+export -f path_output
+
+link_version() # parameter: ${1} current_output_prefix, ${2} new_output_prefix, ${3} file
+{
+    path_out=$(path_output ${3})
+    if [[ -f "${1}${path_out}${3}" ]]; then
+        mkdir -p "${2}${path_out}";
+        ln -s -r "${1}${path_out}${3}" "${2}${path_out}";
+    fi
+}
+export -f link_version  #export it to be accessible to the parallel call
+
+list_local_files() # parameter: ${1} prefix, ${2} 1 to list list all, "" list only '-not -empty'
+{
+    # Returns list of local files, without folder structure
+    if [[ "${ncbi_folders}" -eq 0 ]]; then
+        depth="-maxdepth 1";
+    else
+        depth="-mindepth 4";
+    fi
+    param="-not -empty"
+    if [[ ! -z "${2:-}" ]]; then
+        param=""
+    fi
+    find "${1}${files_dir}" ${depth} ${param} -type f,l -printf "%f\n"
+}
+
 unpack() # parameter: ${1} file, ${2} output folder[, ${3} files to unpack]
 {
     tar xf "${1}" -C "${2}" "${3}"
@@ -530,18 +566,19 @@ export -f print_progress #export it to be accessible to the parallel call
 check_file_folder() # parameter: ${1} url, ${2} log (0->before download/1->after download) - returns 0 (ok) / 1 (error)
 {
     file_name=$(basename ${1})
+    path_name="${target_output_prefix}$(path_output ${file_name})${file_name}"
     # Check if file exists and if it has a size greater than zero (-s)
-    if [ ! -s "${target_output_prefix}${files_dir}${file_name}" ]; then
+    if [ ! -s "${path_name}" ]; then
         if [ "${2}" -eq 1 ]; then echolog "${file_name} download failed [${1}]" "0"; fi
         # Remove file if exists (only zero-sized files)
-        rm -vf "${target_output_prefix}${files_dir}${file_name}" >> "${log_file}" 2>&1
+        rm -vf "${path_name}" >> "${log_file}" 2>&1
         return 1
     else
         if [ "${verbose_log}" -eq 1 ]; then
             if [ "${2}" -eq 0 ]; then 
-                echolog "${file_name} file found on the output folder [${target_output_prefix}${files_dir}${file_name}]" "0"
+                echolog "${file_name} file found on the output folder [${path_name}]" "0"
             else
-                echolog "${file_name} downloaded successfully [${1} -> ${target_output_prefix}${files_dir}${file_name}]" "0"
+                echolog "${file_name} downloaded successfully [${1} -> ${path_name}]" "0"
             fi
         fi
         return 0
@@ -564,11 +601,12 @@ check_md5_ftp() # parameter: ${1} url - returns 0 (ok) / 1 (error)
                 echolog "${file_name} MD5checksum file not available [${md5checksums_url}] - FILE KEPT"  "0"
                 return 0
             else
-                file_md5=$(md5sum ${target_output_prefix}${files_dir}${file_name} | cut -f1 -d' ')
+                path_name="${target_output_prefix}$(path_output ${file_name})${file_name}" # local file path and name
+                file_md5=$(md5sum ${path_name} | cut -f1 -d' ')
                 if [ "${file_md5}" != "${ftp_md5}" ]; then
                     echolog "${file_name} MD5 not matching [${md5checksums_url}] - FILE REMOVED"  "0"
                     # Remove file only when MD5 doesn't match
-                    rm -v "${target_output_prefix}${files_dir}${file_name}" >> ${log_file} 2>&1
+                    rm -v "${path_name}" >> ${log_file} 2>&1
                     return 1
                 else
                     if [ "${verbose_log}" -eq 1 ]; then
@@ -595,7 +633,9 @@ download() # parameter: ${1} url, ${2} job number, ${3} total files, ${4} url_su
         dl=1
     fi
     if [ "${dl}" -eq 1 ]; then # If file is not yet on folder, download it
-        download_url "${1}" "${target_output_prefix}${files_dir}"
+        path_out="${target_output_prefix}$(path_output ${1})"
+        mkdir -p "${path_out}"
+        download_url "${1}" "${path_out}"
         if ! check_file_folder ${1} "1"; then # Check if file was downloaded
             ex=1
         elif ! check_md5_ftp ${1}; then # Check file md5
@@ -668,13 +708,13 @@ remove_files() # parameter: ${1} file, ${2} fields [assembly_accesion,url] OR fi
     fi
     deleted_files=0
     while read f; do
-        fname="${target_output_prefix}${files_dir}${f}"
+        path_name="${target_output_prefix}$(path_output ${f})${f}"
         # Only delete if delete option is enable or if it's a symbolic link (from updates)
-        if [[ -L "${fname}" || "${delete_extra_files}" -eq 1 ]]; then
-            rm "${target_output_prefix}${files_dir}${f}" -v >> ${log_file}
+        if [[ -L "${path_name}" || "${delete_extra_files}" -eq 1 ]]; then
+            rm "${path_name}" -v >> ${log_file}
             deleted_files=$((deleted_files + 1))
         else
-            echolog "kept '${fname}'" "0"
+            echolog "kept '${path_name}'" "0"
         fi
     done <<< "${filelist}"
     echo ${deleted_files}
@@ -682,14 +722,13 @@ remove_files() # parameter: ${1} file, ${2} fields [assembly_accesion,url] OR fi
 
 check_missing_files() # ${1} file, ${2} fields [assembly_accesion,url], ${3} extension - returns assembly accession, url and filename
 {
-    # Just returns if file doesn't exist or if it's zero size
-    list_files ${1} ${2} ${3} | xargs -P "${threads}" --no-run-if-empty -n3 sh -c 'if [ ! -s "'"${target_output_prefix}${files_dir}"'${2}" ]; then echo "${0}'$'\t''${1}'$'\t''${2}"; fi'
+    join -1 3 -2 1 <(list_files ${1} ${2} ${3} | sort -k 3,3 -t$'\t') <(list_local_files "${target_output_prefix}" | sort) -t$'\t' -v 1 -o "1.1,1.2,1.3"
 }
 
 check_complete_record() # parameters: ${1} file, ${2} field [assembly accession, url], ${3} extension - returns assembly accession, url
 {
     expected_files=$(list_files ${1} ${2} ${3} | sort -k 3,3)
-    join -1 3 -2 1 <(echo "${expected_files}" | sort -k 3,3) <(ls -1 "${target_output_prefix}${files_dir}" | sort) -t$'\t' -o "1.1" -v 1 | sort | uniq | # Check for accessions with at least one missing file
+    join -1 3 -2 1 <(echo "${expected_files}" | sort -k 3,3) <(list_local_files "${target_output_prefix}" | sort) -t$'\t' -o "1.1" -v 1 | sort | uniq | # Check for accessions with at least one missing file
     join -1 1 -2 1 <(echo "${expected_files}" | cut -f 1,2 | sort | uniq) - -t$'\t' -v 1 # Extract just assembly accession and url for complete entries (no missing files)
 }
 
@@ -701,8 +740,8 @@ output_assembly_accession() # parameters: ${1} file, ${2} field [assembly access
 output_sequence_accession() # parameters: ${1} file, ${2} field [assembly accession, url], ${3} extension, ${4} mode (A/R), ${5} assembly_summary (for taxid)
 {
     join <(list_files ${1} ${2} "assembly_report.txt" | sort -k 1,1) <(check_complete_record ${1} ${2} ${3} | sort -k 1,1) -t$'\t' -o "1.1,1.3" | # List assembly accession and filename for all assembly_report.txt with complete record (no missing files) - returns assembly accesion, filename
-    join - <(sort -k 1,1 ${5}) -t$'\t' -o "1.1,1.2,2.6" | # Get taxid {1} assembly accesion, {2} filename {3} taxid
-    parallel --tmpdir ${working_dir} --colsep "\t" -j ${threads} -k 'grep "^[^#]" "'"${target_output_prefix}${files_dir}"'{2}" | tr -d "\r" | cut -f 5,7,9 | sed "s/^/{1}\\t/" | sed "s/$/\\t{3}/"' | # Retrieve info from assembly_report.txt and add assemby accession in the beggining and taxid at the end
+    join - <(sort -k 1,1 ${5}) -t$'\t' -o "1.1,1.2,2.6" |     # Get taxid {1} assembly accession, {2} filename {3} taxid
+    parallel --tmpdir ${working_dir} --colsep "\t" -j ${threads} -k 'grep "^[^#]" "${target_output_prefix}$(path_output {2}){2}" | tr -d "\r" | cut -f 5,7,9 | sed "s/^/{1}\\t/" | sed "s/$/\\t{3}/"' | # Retrieve info from assembly_report.txt and add assemby accession in the beggining and taxid at the end
     sed "s/^/${4}\t/" # Add mode A/R at the end    
 }
 
@@ -812,6 +851,7 @@ function showhelp {
     echo $' -B Alternative version label to use as the current version. Mutually exclusive with -i.\n\tCan be used to rollback to an older version or to create multiple branches from a base version.\n\tDefault: ""'
     echo $' -R Number of attempts to retry to download files in batches \n\tDefault: 3'
     echo $' -n Conditional exit status based on number of failures accepted, otherwise will Exit Code = 1.\n\tExample: -n 10 will exit code 1 if 10 or more files failed to download\n\t[integer for file number, float for percentage, 0 = off]\n\tDefault: 0'
+    echo $' -N Output files in folders like NCBI ftp structure (e.g. files/GCF/000/499/605/GCF_000499605.1_EMW001_assembly_report.txt)'
     echo $' -L Downloader\n\t[wget, curl]\n\tDefault: wget'
     echo $' -x Allow the deletion of regular extra files (not symbolic links) found in the output folder'
     echo $' -s Silent output'
@@ -842,6 +882,7 @@ url_list=0
 dry_run=0
 just_fix=0
 conditional_exit=0
+ncbi_folders=0
 silent=0
 silent_progress=0
 debug_mode=0
@@ -856,7 +897,7 @@ downloader_tool="wget"
 
 # Check for required tools
 tool_not_found=0
-tools=( "awk" "bc" "find" "join" "md5sum" "parallel" "sed" "tar" "xargs" "wget" )
+tools=( "awk" "bc" "find" "join" "md5sum" "parallel" "sed" "tar" "wget" )
 for t in "${tools[@]}"
 do
     if [ ! -x "$(command -v ${t})" ]; then
@@ -867,7 +908,7 @@ done
 if [ "${tool_not_found}" -eq 1 ]; then exit 1; fi
 
 # Parse -o and -B first to detect possible updates
-getopts_list="aA:b:B:c:d:D:e:E:f:F:g:hikl:L:mM:n:o:prR:st:T:uVwxZ"
+getopts_list="aA:b:B:c:d:D:e:E:f:F:g:hikl:L:mM:n:No:prR:st:T:uVwxZ"
 OPTIND=1 # Reset getopts
 # Parses working_dir from "$@"
 while getopts "${getopts_list}" opt; do
@@ -933,6 +974,7 @@ while getopts "${getopts_list}" opt "${args[@]}"; do
     m) check_md5=1 ;;
     M) tax_mode=${OPTARG} ;;
     n) conditional_exit=${OPTARG} ;;
+    N) ncbi_folders=1 ;;
     o) working_dir=${OPTARG} ;;
     p) url_list=1 ;;
     r) updated_sequence_accession=1 ;;
@@ -1128,7 +1170,7 @@ else
 fi
 working_dir="$(readlink -m ${working_dir})/"
 files_dir="files/"
-export files_dir working_dir
+export files_dir working_dir ncbi_folders
 
 default_assembly_summary=${working_dir}assembly_summary.txt
 history_file=${working_dir}history.tsv
@@ -1339,7 +1381,8 @@ else # update/fix
 
     echolog "Checking for extra files in the current version [${current_label}]" "1"
     extra=$(tmp_file "extra.tmp")
-    join <(ls -1 "${current_output_prefix}${files_dir}" | sort) <(list_files "${current_assembly_summary}" "1,20" "${file_formats}" | cut -f 3 | sed -e 's/.*\///' | sort) -v 1 > "${extra}"
+    # List local files, "1" to list also empty files
+    join <(list_local_files "${current_output_prefix}" "1" | sort) <(list_files "${current_assembly_summary}" "1,20" "${file_formats}" | cut -f 3 | sed -e 's/.*\///' | sort) -v 1 > "${extra}"
     extra_files=$(count_lines_file "${extra}")
     if [ "${extra_files}" -gt 0 ]; then
         echolog " - ${extra_files} extra files" "1"
@@ -1405,7 +1448,7 @@ else # update/fix
             # Link versions
             echolog "Linking versions [${current_label} --> ${new_label}]" "1"
             # Only link existing files relative to the current version
-            list_files "${current_assembly_summary}" "1,20" "${file_formats}" | cut -f 3 | xargs -P "${threads}" -I{} bash -c 'if [[ -f '"${current_output_prefix}${files_dir}{}"' ]]; then ln -s -r '"${current_output_prefix}${files_dir}{}"' '"${new_output_prefix}${files_dir}"'; fi'
+            list_files "${current_assembly_summary}" "1,20" "${file_formats}" | cut -f 3 | parallel -P "${threads}" link_version "${current_output_prefix}" "${new_output_prefix}" "{}"
             echolog " - Done" "1"
             echolog "" "1"
             # set version - update default assembly summary
@@ -1475,6 +1518,12 @@ else # update/fix
 fi
 
 if [ "${dry_run}" -eq 0 ]; then
+
+    # Clean possible empty folders in NCBI structure after update
+    if [[ "${ncbi_folders}" -eq 1 ]]; then
+        find "${target_output_prefix}${files_dir}" -type d -empty -delete
+    fi
+
     if [ "${download_taxonomy}" -eq 1 ]; then
         echolog "Downloading taxonomy database [${tax_mode}]" "1"
         if [[ "${tax_mode}" == "ncbi" ]]; then
@@ -1496,7 +1545,8 @@ if [ "${dry_run}" -eq 0 ]; then
     fi
 
     expected_files=$(( $(count_lines_file "${default_assembly_summary}")*(n_formats+1) )) # From assembly summary * file formats
-    current_files=$(ls "${target_output_prefix}${files_dir}" | wc -l | cut -f1 -d' ') # From current folder
+    current_files=$(list_local_files "${target_output_prefix}" | wc -l | cut -f1 -d' ') # From current folder
+
     # If is in fixing mode, remove kept extra files from calculation
     if [[ "${extra_files}" -gt 0 && "${just_fix}" -eq 1 ]]; then
         current_files=$(( current_files-extra_files ))
diff --git a/tests/download_test_set.sh b/tests/download_test_set.sh
index 9f37fef..28ecd93 100755
--- a/tests/download_test_set.sh
+++ b/tests/download_test_set.sh
@@ -40,8 +40,10 @@ cut -f 1,6 ${outfld}genomes/*/assembly_summary_*.txt ${outfld}genomes/*/*/assemb
 wget --quiet --show-progress --output-document "${outfld}new_taxdump.tar.gz" "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
 tar xf "${outfld}new_taxdump.tar.gz" -C "${outfld}" taxidlineage.dmp rankedlineage.dmp
 mkdir -p "${outfld}pub/taxonomy/new_taxdump/"
+cat "${outfld}accessions_taxids.txt" | xargs -l bash -c 'grep "^${1}[^0-9]" "'${outfld}'taxidlineage.dmp"' > "${outfld}pub/taxonomy/new_taxdump/taxidlineage.dmp"
 cat "${outfld}accessions_taxids.txt" | xargs -l bash -c 'grep "[^0-9]${1}[^0-9]" "'${outfld}'taxidlineage.dmp"' >> "${outfld}pub/taxonomy/new_taxdump/taxidlineage.dmp"
-cat "${outfld}accessions_taxids.txt" | xargs -l bash -c 'grep "^${1}[^0-9]" "'${outfld}'rankedlineage.dmp"' >> "${outfld}pub/taxonomy/new_taxdump/rankedlineage.dmp"
+cat "${outfld}accessions_taxids.txt" | xargs -l bash -c 'grep "^${1}[^0-9]" "'${outfld}'rankedlineage.dmp"' > "${outfld}pub/taxonomy/new_taxdump/rankedlineage.dmp"
+
 find "${outfld}pub/taxonomy/new_taxdump/" -printf "%P\n" | tar -czf "${outfld}pub/taxonomy/new_taxdump/new_taxdump.tar.gz" --no-recursion -C "${outfld}pub/taxonomy/new_taxdump/" -T -
 md5sum "${outfld}pub/taxonomy/new_taxdump/new_taxdump.tar.gz" > "${outfld}pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5"
 rm "${outfld}new_taxdump.tar.gz" "${outfld}taxidlineage.dmp" "${outfld}rankedlineage.dmp" "${outfld}pub/taxonomy/new_taxdump/taxidlineage.dmp" "${outfld}pub/taxonomy/new_taxdump/rankedlineage.dmp"
diff --git a/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz b/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
index 3f71f0b..8d82ae4 100644
Binary files a/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz and b/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz differ
diff --git a/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5 b/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5
index 4fc09cb..22c17b7 100644
--- a/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5
+++ b/tests/files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5
@@ -1 +1 @@
-a9b0b848349863ab9413d44400f99336  files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
+9ad4e65d12140e0045d3e01f853b8f29  files/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
diff --git a/tests/integration_offline.bats b/tests/integration_offline.bats
index 924ecf8..96df12d 100644
--- a/tests/integration_offline.bats
+++ b/tests/integration_offline.bats
@@ -435,6 +435,7 @@ setup_file() {
 
     # Check if report was printed and has all lines reported
     assert_file_exist ${outdir}${label}/*_assembly_accession.txt
+    assert_file_not_empty ${outdir}${label}/*_assembly_accession.txt
     assert_equal $(count_lines_file ${outdir}${label}/*_assembly_accession.txt) $(count_lines_file ${outdir}assembly_summary.txt)
 }
 
@@ -446,6 +447,18 @@ setup_file() {
 
     # Check if report was printed
     assert_file_exist ${outdir}${label}/*_sequence_accession.txt
+    assert_file_not_empty ${outdir}${label}/*_sequence_accession.txt
+}
+
+@test "Report sequence accession with ncbi folder structure" {
+    outdir=${outprefix}report-sequence-accession-ncbi-folders/
+    label="test"
+    run ./genome_updater.sh -N -d refseq -b ${label} -o ${outdir} -r
+    sanity_check ${outdir} ${label}
+
+    # Check if report was printed
+    assert_file_exist ${outdir}${label}/*_sequence_accession.txt
+    assert_file_not_empty ${outdir}${label}/*_sequence_accession.txt
 }
 
 @test "Report urls" {
@@ -604,7 +617,7 @@ setup_file() {
     sanity_check ${outdir} ${label}
 
     # Remove files to simulate failure
-    rm ${outdir}${label}/files/*
+    rm -rf ${outdir}${label}/files/*
 
     # Dry-run FIX
     run ./genome_updater.sh -d refseq -b ${label} -o ${outdir} -k -i
@@ -639,6 +652,29 @@ setup_file() {
     sanity_check ${outdir} ${label}
 }
 
+@test "Mode UPDATE ncbi folders" {
+    outdir=${outprefix}mode-update-ncbi-folders/
+    label="test"
+
+    # Dry-run NEW
+    run ./genome_updater.sh -N -d refseq -b ${label} -o ${outdir} -k
+    assert_success
+    assert_dir_not_exist ${outdir}
+
+    # Real run NEW
+    run ./genome_updater.sh -N -d refseq -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+
+    # Dry-run UPDATE (use another organism group to simulate change)
+    label="update"
+    run ./genome_updater.sh -N -d refseq -g archaea,fungi -b ${label} -o ${outdir} -k
+    assert_success
+
+    # Real run FIX
+    run ./genome_updater.sh -N -d refseq -g archaea,fungi -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+}
+
 @test "Mode auto UPDATE" {
     outdir=${outprefix}mode-auto-update/
     label="test"
@@ -657,7 +693,7 @@ setup_file() {
     run ./genome_updater.sh -o ${outdir} -b ${label} -k
     assert_success
 
-    # Real run (nothin to update, but carry parameters)
+    # Real run (nothing to update, but carry parameters)
     run ./genome_updater.sh -o ${outdir} -b ${label}
     sanity_check ${outdir} ${label}
 
@@ -677,6 +713,44 @@ setup_file() {
     assert_success
 }
 
+@test "Mode auto UPDATE ncbi folders" {
+    outdir=${outprefix}mode-auto-update-ncbi-folders/
+    label="test"
+
+    # Dry-run NEW
+    run ./genome_updater.sh -N -d refseq -b ${label} -o ${outdir} -g archaea -k
+    assert_success
+    assert_dir_not_exist ${outdir}
+
+    # Real run NEW
+    run ./genome_updater.sh -N -d refseq -b ${label} -o ${outdir} -g archaea
+    sanity_check ${outdir} ${label}
+
+    # Dry-run UPDATE (use same parameters)
+    label="update"
+    run ./genome_updater.sh -N -o ${outdir} -b ${label} -k
+    assert_success
+
+    # Real run (nothing to update, but carry parameters)
+    run ./genome_updater.sh -N -o ${outdir} -b ${label}
+    sanity_check ${outdir} ${label}
+
+    # Dry-run UPDATE
+    label="update2"
+    run ./genome_updater.sh -N -o ${outdir} -b ${label} -g "" -d refseq,genbank -u -k
+    assert_success
+
+    # Real run FIX, remove org (get all), add database, add bool report
+    run ./genome_updater.sh -N -o ${outdir} -b ${label} -g "" -d refseq,genbank -u
+    sanity_check ${outdir} ${label}
+
+    assert_file_exist ${outdir}${label}/*_assembly_accession.txt
+
+    # Check log for updates
+    grep "0 updated, [1-9][0-9]* removed, [1-9][0-9]* new entries" ${outdir}${label}/*.log # >&3
+    assert_success
+}
+
 @test "Tax. Mode GTDB" {
     outdir=${outprefix}tax-gtdb/
     label="test"
@@ -703,3 +777,44 @@ setup_file() {
     run ./genome_updater.sh -o ${outdir} -b ${label} -e ${files_dir}simulated/assembly_summary_invalid_xCF.txt
     assert_failure
 }
+
+@test "NCBI folders" {
+    outdir=${outprefix}ncbi-folders/
+    label="1-refseq"
+    run ./genome_updater.sh -N -d refseq -g archaea -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+
+    # refseq base folder is created, no genbank
+    assert_dir_exist "${outdir}${label}/files/GCF/"
+    assert_dir_not_exist "${outdir}${label}/files/GCA/"
+
+    # Add genbank
+    label="2-refseq-genbank"
+    run ./genome_updater.sh -N -d refseq,genbank -g archaea -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+
+    # refseq and genbank base folders are created
+    assert_dir_exist "${outdir}${label}/files/GCF/"
+    assert_dir_exist "${outdir}${label}/files/GCA/"
+   
+    # Remove refseq
+    label="3-genbank"
+    run ./genome_updater.sh -N -d genbank -g archaea -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+
+    assert_dir_not_exist "${outdir}${label}/files/GCF/"
+    assert_dir_exist "${outdir}${label}/files/GCA/"
+
+    # no empty folders
+    assert_equal $(find "${outdir}${label}/files/" -type d -empty | wc -l | cut -f1 -d' ') 0
+    
+    # Update without -N, do not consider folder structute and download again to base files folde
+    # Remove refseq
+    label="4-no-ncbi-folders"
+    run ./genome_updater.sh -d genbank -g archaea -b ${label} -o ${outdir}
+    sanity_check ${outdir} ${label}
+
+    # refseq and genbank are no longer
+    assert_dir_not_exist "${outdir}${label}/files/GCF/"
+    assert_dir_not_exist "${outdir}${label}/files/GCA/"
+}
\ No newline at end of file
diff --git a/tests/integration_online.bats b/tests/integration_online.bats
index bc7bce6..b03d01a 100644
--- a/tests/integration_online.bats
+++ b/tests/integration_online.bats
@@ -45,12 +45,12 @@ setup_file() {
     # Protozoa in refseq is the smallest available assembly_summary at the time of writing this test (01.2022)
     # 5820 genus Plasmodium
     label_genus="genus"
-    run ./genome_updater.sh -d refseq -g protozoa -T 5820 -b ${label_genus} -t ${threads} -o ${outdir}
+    run ./genome_updater.sh -N -d refseq -g protozoa -T 5820 -b ${label_genus} -t ${threads} -o ${outdir}
     sanity_check ${outdir} ${label_genus}
 
     # 5794 phylum Apicomplexa
     label_phylum="phylum"
-    run ./genome_updater.sh -d refseq -g protozoa -T 5794 -b ${label_phylum} -t ${threads} -o ${outdir}
+    run ./genome_updater.sh -N -d refseq -g protozoa -T 5794 -b ${label_phylum} -t ${threads} -o ${outdir}
     sanity_check ${outdir} ${label_phylum}
     
     # More files filtering by phylum than genus
diff --git a/tests/libs/bats b/tests/libs/bats
index 210acf3..6636e2c 160000
--- a/tests/libs/bats
+++ b/tests/libs/bats
@@ -1 +1 @@
-Subproject commit 210acf3a8ed318ddedad3137c15451739beba7d4
+Subproject commit 6636e2c2ef5ffe361535cb45fc61682c5ef46b71
diff --git a/tests/libs/bats-assert b/tests/libs/bats-assert
index e0de84e..78fa631 160000
--- a/tests/libs/bats-assert
+++ b/tests/libs/bats-assert
@@ -1 +1 @@
-Subproject commit e0de84e9c011223e7f88b7ccf1c929f4327097ba
+Subproject commit 78fa631d1370562d2cd4a1390989e706158e7bf0
diff --git a/tests/libs/bats-file b/tests/libs/bats-file
index 17fa557..805ffb7 160000
--- a/tests/libs/bats-file
+++ b/tests/libs/bats-file
@@ -1 +1 @@
-Subproject commit 17fa557f6fe28a327933e3fa32efef1d211caa5a
+Subproject commit 805ffb74fe085fd7be4fe43d787387b20d4bd7b6
diff --git a/tests/utils.bash b/tests/utils.bash
index f27f3d2..a388d36 100644
--- a/tests/utils.bash
+++ b/tests/utils.bash
@@ -9,11 +9,11 @@ count_lines_file(){ # $1 file
 }
 
 count_files() { # $1 outdir, $2 label
-    ls_files ${1} ${2} | wc -l | cut -f1 -d' '
+    find_files ${1} ${2} | wc -l | cut -f1 -d' '
 }
 
-ls_files() { # $1 outdir, $2 label
-    ls -1 ${1}${2}/files/*
+find_files() { # $1 outdir, $2 label
+    find ${1}${2}/files/ -type f,l
 }
 
 sanity_check() { # $1 outdir, $2 label, [$3 number of file types]
@@ -37,7 +37,7 @@ sanity_check() { # $1 outdir, $2 label, [$3 number of file types]
     # Check file count based on assembly_summary
     assert_equal $(count_files ${1} ${2}) $(($(count_lines_file ${1}assembly_summary.txt) * ${nfiles}))
     # Check files in folder (if any)
-    for file in $(ls_files ${1} ${2}); do
+    for file in $(find_files ${1} ${2}); do
         assert_file_not_empty $file
     done