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collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.

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nextgenusfs/genome_scripts

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ITSx2tbl.py
ITSx2tbl.py
 
 
JAAWS.sh
JAAWS.sh
 
 
JAAWS_ion.sh
JAAWS_ion.sh
 
 
README.md
README.md
 
 
afumi_combine_annotation.py
afumi_combine_annotation.py
 
 
antismash2clusters.py
antismash2clusters.py
 
 
bold2utax.py
bold2utax.py
 
 
busco2raxml.py
busco2raxml.py
 
 
cat_fasta.py
cat_fasta.py
 
 
cluster2utax.py
cluster2utax.py
 
 
contamination_screen.sh
contamination_screen.sh
 
 
contig_cleaner.py
contig_cleaner.py
 
 
csv2heatmap.py
csv2heatmap.py
 
 
fasta2raxml.py
fasta2raxml.py
 
 
fasta_grepheader.py
fasta_grepheader.py
 
 
fasta_keep.py
fasta_keep.py
 
 
fasta_remove.py
fasta_remove.py
 
 
fasta_stats.py
fasta_stats.py
 
 
fastq_stats.py
fastq_stats.py
 
 
filter_tbl.py
filter_tbl.py
 
 
findHMM.py
findHMM.py
 
 
fix_encoding.pl
fix_encoding.pl
 
 
format_fungidb.sh
format_fungidb.sh
 
 
format_jgi.sh
format_jgi.sh
 
 
format_jgi_kog.sh
format_jgi_kog.sh
 
 
gb2all.py
gb2all.py
 
 
gb2dna.py
gb2dna.py
 
 
gb2gff.py
gb2gff.py
 
 
gb2products.py
gb2products.py
 
 
gb2proteinortho.py
gb2proteinortho.py
 
 
gb2proteins.py
gb2proteins.py
 
 
gb2smurf.py
gb2smurf.py
 
 
gb2stats.py
gb2stats.py
 
 
gb2tab.py
gb2tab.py
 
 
gb_remove_records.py
gb_remove_records.py
 
 
gb_slice.py
gb_slice.py
 
 
gb_stats.py
gb_stats.py
 
 
gbk2folders.py
gbk2folders.py
 
 
getHMMdomains.py
getHMMdomains.py
 
 
get_HMM_domains.pl
get_HMM_domains.pl
 
 
get_coverage.sh
get_coverage.sh
 
 
get_ncbi_genomes.py
get_ncbi_genomes.py
 
 
gff_convert.py
gff_convert.py
 
 
iBOL2utax.py
iBOL2utax.py
 
 
ion_uparse.sh
ion_uparse.sh
 
 
jgi2gbk.sh
jgi2gbk.sh
 
 
mafft2raxml.py
mafft2raxml.py
 
 
pilon.sh
pilon.sh
 
 
prot_ortho_draw_tree.sh
prot_ortho_draw_tree.sh
 
 
proteome_compare.py
proteome_compare.py
 
 
qPCR2dilutions.py
qPCR2dilutions.py
 
 
redraw_karyotype.sh
redraw_karyotype.sh
 
 
reformat_fasta_headers.pl
reformat_fasta_headers.pl
 
 
reformat_seqs.py
reformat_seqs.py
 
 
rename_tree.pl
rename_tree.pl
 
 
run_allmaps.sh
run_allmaps.sh
 
 
seq_length.py
seq_length.py
 
 
sleuth2table.py
sleuth2table.py
 
 
smurf_reformat.pl
smurf_reformat.pl
 
 
snippy2bed.py
snippy2bed.py
 
 
snippy2indelavg.py
snippy2indelavg.py
 
 
snippy2stats.py
snippy2stats.py
 
 
snippy2tree.py
snippy2tree.py
 
 
sort_fasta.py
sort_fasta.py
 
 
sort_rename_fasta.py
sort_rename_fasta.py
 
 
test.sbt
test.sbt
 
 

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genome_scripts

collection of random scripts for processing genome related files. the shell scripts are specific to my environment and are not meant to be used elsewhere, so likely heavy editing will be needed to run on another system

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collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.

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