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Dockerfiles
Dockerfiles
 
 
lib
lib
 
 
old
old
 
 
.gitignore
.gitignore
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
agp2fasta.py
agp2fasta.py
 
 
alnfa_cut.py
alnfa_cut.py
 
 
alnfa_remove_invariant.py
alnfa_remove_invariant.py
 
 
assembly_rmdup.py
assembly_rmdup.py
 
 
bam2fq_by_readname.py
bam2fq_by_readname.py
 
 
bam_renameChr.py
bam_renameChr.py
 
 
bam_stats.py
bam_stats.py
 
 
cds_codon_usage.py
cds_codon_usage.py
 
 
dagchainer_from_orthofinder.py
dagchainer_from_orthofinder.py
 
 
deepsignal_CpG_calls_to_bed.py
deepsignal_CpG_calls_to_bed.py
 
 
dna2sixframe.py
dna2sixframe.py
 
 
fast5_check.py
fast5_check.py
 
 
fasta_GCcontent_bed.py
fasta_GCcontent_bed.py
 
 
fasta_concatenate.py
fasta_concatenate.py
 
 
fasta_findN.py
fasta_findN.py
 
 
fasta_id_filter.py
fasta_id_filter.py
 
 
fasta_make_windows.py
fasta_make_windows.py
 
 
fasta_pairwise_identity.py
fasta_pairwise_identity.py
 
 
fasta_remove_clone.py
fasta_remove_clone.py
 
 
fasta_rename.py
fasta_rename.py
 
 
fasta_sort.py
fasta_sort.py
 
 
fasta_stats.py
fasta_stats.py
 
 
fasta_wrap_line.py
fasta_wrap_line.py
 
 
fastq_check_dups.py
fastq_check_dups.py
 
 
fastq_check_platform.py
fastq_check_platform.py
 
 
fastq_check_qual.py
fastq_check_qual.py
 
 
fastq_dedup.py
fastq_dedup.py
 
 
fastq_estimate_InsertSize.py
fastq_estimate_InsertSize.py
 
 
fastq_interleave.py
fastq_interleave.py
 
 
fastq_stats.cpp
fastq_stats.cpp
 
 
fastq_stats.jl
fastq_stats.jl
 
 
fastq_stats.py
fastq_stats.py
 
 
fastx_filter.py
fastx_filter.py
 
 
gff2fa.py
gff2fa.py
 
 
gff_to_genoplotr_tab.py
gff_to_genoplotr_tab.py
 
 
guppy_barcode_summary.py
guppy_barcode_summary.py
 
 
iterative_NextPolish.py
iterative_NextPolish.py
 
 
iterative_pilon.py
iterative_pilon.py
 
 
iterative_racon.py
iterative_racon.py
 
 
megalodon_paired_output.py
megalodon_paired_output.py
 
 
mfannot_tbl_to_gff.py
mfannot_tbl_to_gff.py
 
 
mummer_wrapper.sh
mummer_wrapper.sh
 
 
ncbi_fetch_seq.py
ncbi_fetch_seq.py
 
 
orf_finder.py
orf_finder.py
 
 
orthofinder_gene_to_OG.py
orthofinder_gene_to_OG.py
 
 
orthofinder_rename_OG.py
orthofinder_rename_OG.py
 
 
plink_dist_to_phylip.py
plink_dist_to_phylip.py
 
 
plot_coverage.R
plot_coverage.R
 
 
qwrap.py
qwrap.py
 
 
recircularize_fasta.py
recircularize_fasta.py
 
 
recircularize_gff.py
recircularize_gff.py
 
 
remove_log.sh
remove_log.sh
 
 
repeatmasker_PerBaseBest.py
repeatmasker_PerBaseBest.py
 
 
repeatmasker_to_bed.py
repeatmasker_to_bed.py
 
 
rip_finder.py
rip_finder.py
 
 
run_Haplomerger2.sh
run_Haplomerger2.sh
 
 
run_genomescope.sh
run_genomescope.sh
 
 
run_guppy.sh
run_guppy.sh
 
 
run_purge_dups.sh
run_purge_dups.sh
 
 
run_purge_haplotigs.sh
run_purge_haplotigs.sh
 
 
slack_notify.py
slack_notify.py
 
 
ssh_twnia.py
ssh_twnia.py
 
 
trf_telomere_finder.py
trf_telomere_finder.py
 
 
uc_info.py
uc_info.py
 
 
uc_split_fasta_by_cluster.py
uc_split_fasta_by_cluster.py
 
 
vcf_estimate_QV.py
vcf_estimate_QV.py
 
 
vcf_getMAF.py
vcf_getMAF.py
 
 
vcf_to_fa.py
vcf_to_fa.py
 
 
waitpid.sh
waitpid.sh
 
 
whatshap_stats.py
whatshap_stats.py
 
 

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My_scripts

Simple scripts for analysis

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Simple scripts for bioinformatics

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