bio.txt

Bifrost
CrossMap.py
DAS_Tool
ExpansionHunter
GUESSmyLT
Genrich
GraphAligner
MBG
MethylDackel
NanoFilt
NanoPlot
NanoStat
ProcessRepeats
RepeatMasker
RepeatModeler
RepeatProteinMask
STAR
STAR-Fusion
SnpSift
TransDecoder.LongOrfs
TransDecoder.Predict
Trinity
abba-baba
abricate
abundance-dist-single.py
abundance-dist.py
abyss-align
abyss-bloom
abyss-fac
abyss-fixmate
abyss-index
abyss-map
abyss-pe
agat
agat_convert_bed2gff.pl
agat_convert_embl2gff.pl
agat_convert_genscan2gff.pl
agat_convert_mfannot2gff.pl
agat_convert_minimap2_bam2gff.pl
agat_convert_sp_gff2bed.pl
agat_convert_sp_gff2gtf.pl
agat_convert_sp_gff2tsv.pl
agat_convert_sp_gff2zff.pl
agat_convert_sp_gxf2gxf.pl
agat_sp_Prokka_inferNameFromAttributes.pl
agat_sp_add_attribute_shortest_exon_size.pl
agat_sp_add_attribute_shortest_intron_size.pl
agat_sp_add_introns.pl
agat_sp_add_start_and_stop.pl
agat_sp_alignment_output_style.pl
agat_sp_clipN_seqExtremities_and_fixCoordinates.pl
agat_sp_compare_two_BUSCOs.pl
agat_sp_compare_two_annotations.pl
agat_sp_complement_annotations.pl
agat_sp_ensembl_output_style.pl
agat_sp_extract_attributes.pl
agat_sp_extract_sequences.pl
agat_sp_filter_by_ORF_size.pl
agat_sp_filter_by_locus_distance.pl
agat_sp_filter_by_mrnaBlastValue.pl
agat_sp_filter_feature_by_attribute_presence.pl
agat_sp_filter_feature_by_attribute_value.pl
agat_sp_filter_feature_from_keep_list.pl
agat_sp_filter_feature_from_kill_list.pl
agat_sp_filter_gene_by_intron_numbers.pl
agat_sp_filter_gene_by_length.pl
agat_sp_filter_incomplete_gene_coding_models.pl
agat_sp_filter_record_by_coordinates.pl
agat_sp_fix_cds_phases.pl
agat_sp_fix_features_locations_duplicated.pl
agat_sp_fix_fusion.pl
agat_sp_fix_longest_ORF.pl
agat_sp_fix_overlaping_genes.pl
agat_sp_fix_small_exon_from_extremities.pl
agat_sp_flag_premature_stop_codons.pl
agat_sp_flag_short_introns.pl
agat_sp_functional_statistics.pl
agat_sp_keep_longest_isoform.pl
agat_sp_kraken_assess_liftover.pl
agat_sp_list_short_introns.pl
agat_sp_load_function_from_protein_align.pl
agat_sp_manage_IDs.pl
agat_sp_manage_UTRs.pl
agat_sp_manage_attributes.pl
agat_sp_manage_functional_annotation.pl
agat_sp_manage_introns.pl
agat_sp_merge_annotations.pl
agat_sp_prokka_fix_fragmented_gene_annotations.pl
agat_sp_sensitivity_specificity.pl
agat_sp_separate_by_record_type.pl
agat_sp_statistics.pl
agat_sp_webApollo_compliant.pl
agat_sq_add_attributes_from_tsv.pl
agat_sq_add_hash_tag.pl
agat_sq_add_locus_tag.pl
agat_sq_count_attributes.pl
agat_sq_filter_feature_from_fasta.pl
agat_sq_list_attributes.pl
agat_sq_manage_IDs.pl
agat_sq_manage_attributes.pl
agat_sq_mask.pl
agat_sq_remove_redundant_entries.pl
agat_sq_repeats_analyzer.pl
agat_sq_reverse_complement.pl
agat_sq_rfam_analyzer.pl
agat_sq_split.pl
agat_sq_stat_basic.pl
alignmentSieve
alimask
anacapa_QC_dada2.sh
annotatePeaks.pl
any2fasta
archive-pubmed
assess_assembly
assess_homopolymers
bFst
backtranambig
backtranseq
badread
bakta
bamCompare
bamCoverage
bamPEFragmentSize
bamtools
barrnap
bcftools
bedGraphToBigWig
bedops
bedtools
bgzip
bigwigCompare
bio
bioawk
bismark
blastdbcheck
blastdbcmd
blastn
blastp
blastx
blat
blobtools
bonito
bowtie2
bowtie2-build
bowtie2-inspect
brename
busco
bwa
bwa-mem2
canu
catalogue_errors
cd-hit
cd-hit-2d
cd-hit-454
cd-hit-est
cd-hit-est-2d
cellranger
centrifuge
checkm
circlator
clustalo
cnvkit.py
combineMUMs
common_errors_from_bam
compare-ddbj
compleasm
computeGCBias
computeMatrix
computeMatrixOperations
configManta.py
configureStrelkaGermlineWorkflow.py
configureStrelkaSomaticWorkflow.py
convert-sam-for-rsem
coronaspades.py
correctGCBias
coverage_from_bam
coverage_from_fastx
cpgplot
cromwell
csvclean
csvcut
csvformat
csvgrep
csvjoin
csvjson
csvlook
csvpy
csvsort
csvsql
csvstack
csvstat
csvtk
cuffcompare
cuffdiff
cufflinks
cuffmerge
cuffnorm
cuffquant
cutadapt
cuteSV
cuttlefish
dRep
dataformat
datasets
datatool
delly
delta-filter
dfast
diamond
dnaapler
dnadiff
do-partition.py
download-ncbi-data
download_eggnog_data.py
dragonflye
duphold
dwgsim
dwgsim_eval
easel
edirect
edirutil
efetch
efilter
einfo
elink
elprep
emapper.py
enotify
entrez-phrase-search
epost
esearch
estimateReadFiltering
estimateScaleFactor
esummary
extract-paired-reads.py
extract-transcript-to-gene-map-from-trinity
faToTwoBit
falco
fast_convert
fasterq-dump
fastp
fastq-dump
fastqc
fastqe
fastqp
fasttree
featureCounts
fetch-pubmed
ffq
filter-abund-single.py
filter-abund.py
filtlong
findMotifs.pl
findMotifsGenome.pl
find_indels
flye
foldseek
freebayes
gatk
gdc-client
genbank-to-ddbj
genotypeSummary
gfatools
gff3-to-ddbj
gffread
gffutils-cli
glnexus_cli
graphlan.py
gridss
gt
guppy_basecaller
hailctl
hap.py
hapLrt
hhblits
hifiasm
hisat2
hisat2-build
hisat2-inspect
hisat2_extract_exons.py
hisat2_extract_snps_haplotypes_UCSC.py
hisat2_extract_snps_haplotypes_VCF.py
hisat2_extract_splice_sites.py
hisat2_simulate_reads.py
hmmalign
hmmbuild
hmmconvert
hmmemit
hmmfetch
hmmlogo
hmmpgmd
hmmpgmd_shard
hmmpress
hmmscan
hmmsearch
hmmsim
hmmstat
htseq-count
htsfile
humann
hypo
iHS
in2csv
index-pubmed
interproscan.sh
intersect_assembly_errors
iqtree
ivar
j2x
jackhmmer
jellyfish
kaiju
kalign
kallisto
kmc
kmc_dump
kmc_tools
kmcp
kneaddata
kraken
kraken2
kraken2-build
krakenuniq
krakenuniq-build
krakenuniq-download
load-graph.py
load-into-counting.py
loadPromoters.pl
lofreq
long_fastx
lumpy
lumpyexpress
macs2
macs3
mafft
magicblast
makeblastdb
makehmmerdb
mapper.pl
mash
mashmap
masurca
medaka
medaka_consensus
medaka_counts
medaka_haploid_variant
megacc
megahit
meltEHH
merqury.sh
metabat
metaphlan
metaplatanus
metaquast
metaspades.py
mgaps
miRDeep2.pl
mini_align
mini_assemble
miniasm
minigraph
minimap2
minipolish
miniprot
mlst
mmseqs
mosdepth
motus
multiBamSummary
multiBigwigSummary
multiqc
mummer
mummerplot
muscle
mview
nanopolish
nanoq
nextDenovo
nextPolish
nextflow
nextstrain
nhmmer
nhmmscan
normalize-by-median.py
normalize-iHS
nquire
ntedit
nucmer
nullarbor.pl
octopus
pFst
pVst
paftools.js
pangolin
pepinfo
permuteGPAT++
permuteSmooth
phmmer
phylophlan
pilon
pindel
planemo
plasmidspades.py
plass
platanus_b
plink
plotCorrelation
plotCoverage
plotEnrichment
plotFingerprint
plotHaps
plotHeatmap
plotPCA
plotProfile
polca.sh
polypolish
pomoxis_path
popStats
porechop
prefetch
primer3_core
primer3_masker
prokka
promer
psiblast
pyega3
pysradb
qiime
qscores_from_summary
quantifier.pl
quast
quast-lg.py
racon
raven
ref_seqs_from_bam
remora
rename
repeat-match
reverse_bed
rnaspades.py
rnaviralspades.py
rpsblast
rsem-bam2readdepth
rsem-bam2wig
rsem-build-read-index
rsem-calculate-credibility-intervals
rsem-calculate-expression
rsem-control-fdr
rsem-extract-reference-transcripts
rsem-for-ebseq-calculate-clustering-info
rsem-for-ebseq-find-DE
rsem-for-ebseq-generate-ngvector-from-clustering-info
rsem-gen-transcript-plots
rsem-generate-data-matrix
rsem-get-unique
rsem-gff3-to-gtf
rsem-parse-alignments
rsem-plot-model
rsem-plot-transcript-wiggles
rsem-prepare-reference
rsem-preref
rsem-refseq-extract-primary-assembly
rsem-run-ebseq
rsem-run-em
rsem-run-gibbs
rsem-sam-validator
rsem-scan-for-paired-end-reads
rsem-simulate-reads
rsem-synthesis-reference-transcripts
rsem-tbam2gbam
run_MaxBin.pl
salmon
sambamba
samtools
segmentFst
segmentIhs
seqfu
seqkit
seqmagick
seqret
seqtk
sequenceDiversity
shasta
shovill
show-aligns
show-coords
show-diff
show-snps
show-tiling
skesa
smof
smoother
snakemake
sniffles
snippy
snpEff
som.py
somalier
sortmerna
spades-gbuilder
spades-gmapper
spades-kmer-estimating
spades-kmercount
spades-read-filter
spades.py
spaligner
spliceai
split_fastx
sql2csv
sra-stat
srapath
stats_from_bam
strainphlan
stringtie
subread-align
subread-buildindex
subsample_bam
summary_from_stats
svim-asm
svtools
svtyper
svtyper-sso
tabix
tag_bam
taxonkit
tblastn
tblastx
toil
transmute
treetime
trim-low-abund.py
trim_alignments
trim_galore
trimmomatic
trycycler
unicycler
unicycler_align
unicycler_check
unicycler_polish
unicycler_scrub
unikmer
union
unique-kmers.py
varscan
vcf2dag
vcf2fasta
vcfallelicprimitives
vcfanno
vcfannotate
vcfcheck
vcfcombine
vcfentropy
vcfevenregions
vcffilter
vcfgeno2haplo
vcfglbound
vcfglxgt
vcfinfosummarize
vcfintersect
vcfld
vcfleftalign
vcfprimers
vcfrandomsample
vcfremap
vcfroc
vcfsample2info
vcfsamplediff
vcfstats
vcfstreamsort
vcftools
vdb-config
velvetg
velveth
vep
verkko
vg
vsearch
wcFst
wgsim
wigToBigWig
winnowmap
wtdbg2
xtract
yak
zindex
zq