BIOINFORMATICS BINARIES

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BIOINFORMATICS BINARIES

This repository contains all binaries relevant to bioinfo work. Most originate from neptune:/users/tg/lpryszcz/bin

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BIOINFORMATICS BINARIES

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Name		Name	Last commit message	Last commit date
Latest commit History 512 Commits
python_modules		python_modules
teaching		teaching
#fastq2kmers.py#		#fastq2kmers.py#
.gitignore		.gitignore
BRH.py		BRH.py
FastaIndex.py		FastaIndex.py
LICENCE.txt		LICENCE.txt
README		README
README.md		README.md
SOLiD2Std.pl		SOLiD2Std.pl
SraTailor		SraTailor
TE_analysis.py		TE_analysis.py
a.out		a.out
abi2fastq.py		abi2fastq.py
annotated_chromosomes.py		annotated_chromosomes.py
archive_data_ont.sh		archive_data_ont.sh
augustus_gff2fasta.py		augustus_gff2fasta.py
backup_crg.sh		backup_crg.sh
bam2RNAediting.py		bam2RNAediting.py
bam2amplicons.py		bam2amplicons.py
bam2bigwig.py		bam2bigwig.py
bam2cnv.py		bam2cnv.py
bam2counts.py		bam2counts.py
bam2cov.py		bam2cov.py
bam2cov.py_bck		bam2cov.py_bck
bam2cov_multi_pool.py		bam2cov_multi_pool.py
bam2cov_pool.py		bam2cov_pool.py
bam2coverage.py		bam2coverage.py
bam2difference.py		bam2difference.py
bam2editing_penetrance.py		bam2editing_penetrance.py
bam2enhancers.py		bam2enhancers.py
bam2heterozygous.py		bam2heterozygous.py
bam2mitochondrial.py		bam2mitochondrial.py
bam2paternal.py		bam2paternal.py
bam2ploidy.py		bam2ploidy.py
bam2select.py		bam2select.py
bam2snps.py		bam2snps.py
bam2snps.ref.py		bam2snps.ref.py
bam2split.py		bam2split.py
bam2stats.py		bam2stats.py
bam2stats.sh		bam2stats.sh
bam2stranded.py		bam2stranded.py
bam2sv.py		bam2sv.py
bam2transcript_completeness.py		bam2transcript_completeness.py
bam2vcf.py		bam2vcf.py
barcode2fqname.py		barcode2fqname.py
bash_set_variables		bash_set_variables
bed2RNALfold.py		bed2RNALfold.py
bed2cnv.py		bed2cnv.py
bed2cnv_plot.py		bed2cnv_plot.py
bed2count_filter.py		bed2count_filter.py
bed2graph.py		bed2graph.py
bed2igv_batch.py		bed2igv_batch.py
bed2region.py		bed2region.py
bed2stats.py		bed2stats.py
bedGraphToBigWig		bedGraphToBigWig
bedcount2plot.py		bedcount2plot.py
blast2hits.py		blast2hits.py
blast2matrix.py		blast2matrix.py
blast2nohit.py		blast2nohit.py
blastout2identity.py		blastout2identity.py
blastout2profile.py		blastout2profile.py
blat		blat
blat2collapse.py		blat2collapse.py
boxplot.py		boxplot.py
brh.py		brh.py
bright.sh		bright.sh
clean_root.sh		clean_root.sh
clean_snap.sh		clean_snap.sh
combine_windows.py		combine_windows.py
composer		composer
composer.phar		composer.phar
contig2gc.py		contig2gc.py
coords2ordered.py		coords2ordered.py
counts2cnv.mean.py		counts2cnv.mean.py
counts2cnv.py		counts2cnv.py
coverage_graph.py		coverage_graph.py
coverage_track.py		coverage_track.py
csv2common.py		csv2common.py
csv2fasta.py		csv2fasta.py
csv2xls.py		csv2xls.py
cuffdiff2de.py		cuffdiff2de.py
decypher2bed.py		decypher2bed.py
deseq2annotate.py		deseq2annotate.py
deseq2de.py		deseq2de.py
docker-compose		docker-compose
dropbox-crg		dropbox-crg
du.sh		du.sh
duptree		duptree
embl2fasta.py		embl2fasta.py
embl2gb.py		embl2gb.py
embl2gff.pl		embl2gff.pl
embl2gtf.py		embl2gtf.py
embl2protein.py		embl2protein.py
ena_download_and_rename.py		ena_download_and_rename.py
exonerate		exonerate
exonerate2ptc.py		exonerate2ptc.py
exonerategff2gtf.py		exonerategff2gtf.py
fast52reads.py		fast52reads.py
fast5_to_fastq.py		fast5_to_fastq.py
fasta2GC.py		fasta2GC.py
fasta2GCplot.py		fasta2GCplot.py
fasta2agp.py		fasta2agp.py
fasta2clusters.py		fasta2clusters.py
fasta2concatenated.py		fasta2concatenated.py
fasta2contigs.py		fasta2contigs.py
fasta2diverged.py		fasta2diverged.py
fasta2fastq.py		fasta2fastq.py
fasta2gaps.py		fasta2gaps.py
fasta2gc.py		fasta2gc.py
fasta2homozygous.py		fasta2homozygous.py
fasta2loh.py		fasta2loh.py
fasta2softmasked.py		fasta2softmasked.py
fasta2unmask.py		fasta2unmask.py
fasta_stats.py		fasta_stats.py
fastq2fasta.py		fastq2fasta.py
fastq2fastq.py		fastq2fastq.py
fastq2kmers.py		fastq2kmers.py
fastq2random.py		fastq2random.py
fastq2repeats.py		fastq2repeats.py
fastq2shuffledFastQ.py		fastq2shuffledFastQ.py
fastq2shuffledFasta.py		fastq2shuffledFasta.py
fastq2sspace.bwamem.py		fastq2sspace.bwamem.py
fastq2sspace.py		fastq2sspace.py
fastq2sspace_bwamem.py		fastq2sspace_bwamem.py
fastq2telomers.py		fastq2telomers.py
fastq2trim.py		fastq2trim.py
fastq_select.py		fastq_select.py
fastx2reverse.py		fastx2reverse.py
fastx2reverse_complement.py		fastx2reverse_complement.py
filterReads.new.py		filterReads.new.py
filter_by_coverage.py		filter_by_coverage.py
filter_fasta.py		filter_fasta.py
find_telomers.py		find_telomers.py
fluxgtf2counts.py		fluxgtf2counts.py
fpkm2expression_plot.py		fpkm2expression_plot.py
fpkm2major.py		fpkm2major.py
fqextract		fqextract
fqextract.c		fqextract.c
fqextract.py		fqextract.py
fqextract_not.py		fqextract_not.py
gb2embl.py		gb2embl.py
gb2fasta.py		gb2fasta.py
gb2gtf.py		gb2gtf.py
gb2protein.py		gb2protein.py
gem.py		gem.py
genbank2fasta.py		genbank2fasta.py
gene2go.py		gene2go.py
gene2selected.py		gene2selected.py
genePredToGtf		genePredToGtf
geneid2genename.py		geneid2genename.py
genemark2bed.py		genemark2bed.py
genemark2bedGraph.py		genemark2bedGraph.py
genome_graph.py		genome_graph.py
genome_track.py		genome_track.py
get_complete_genomes.NCBI.py		get_complete_genomes.NCBI.py
get_fragmented_assemblies.py		get_fragmented_assemblies.py
get_polyA.py		get_polyA.py
gff2bed.py		gff2bed.py
grep.py		grep.py
gtf2bed.py		gtf2bed.py
gtf2bed_transcripts.py		gtf2bed_transcripts.py
gtf2embl.py		gtf2embl.py
gtf2fasta.py		gtf2fasta.py
heterozygous2fasta.py		heterozygous2fasta.py
hibernate.sh		hibernate.sh
identity_density.py		identity_density.py
idxstats2copynumber.py		idxstats2copynumber.py
idxstats2coverage.py		idxstats2coverage.py
idxstats2species.py		idxstats2species.py
igv2		igv2
insertSize.py		insertSize.py
insert_estimation.py		insert_estimation.py
insert_size_plot.py		insert_size_plot.py
interpro_tsv2function.py		interpro_tsv2function.py
interpro_tsv2go.py		interpro_tsv2go.py
intersect2bed.py		intersect2bed.py
isoforms2longest.py		isoforms2longest.py
khash.h		khash.h
kmc		kmc
kmc_dump		kmc_dump
kmer2count.py		kmer2count.py
last-sam-mark-supplementary.py		last-sam-mark-supplementary.py
lastal_mark_supplementary.py		lastal_mark_supplementary.py
latexencode.py		latexencode.py
len2n50.py		len2n50.py
liftOver		liftOver
load_dump.sh		load_dump.sh
local_assembly.py		local_assembly.py
local_assembly.simple.bowtie2.py		local_assembly.simple.bowtie2.py
local_assembly.simple.bwamem.py		local_assembly.simple.bwamem.py
local_assembly.simple.py		local_assembly.simple.py
loh2chrom.py		loh2chrom.py
low_disk_monit.sh		low_disk_monit.sh
lsfd.sh		lsfd.sh
memusage.sh		memusage.sh
modifications2rna.py		modifications2rna.py
modifications2signatures.py		modifications2signatures.py
mpileup2baf.pl		mpileup2baf.pl
n50.py		n50.py
newick2rooted.py		newick2rooted.py
nextseq.py		nextseq.py
nextseq.sh		nextseq.sh
nucmer2ordered.py		nucmer2ordered.py
nw2species.py		nw2species.py
oslay		oslay
pbsim		pbsim
pbsim.model_qc_ccs		pbsim.model_qc_ccs
pbsim.model_qc_clr		pbsim.model_qc_clr
pfam2gtf.py		pfam2gtf.py
phylome2nSizeFamilies.py		phylome2nSizeFamilies.py
phylome2orthologous_groups.py		phylome2orthologous_groups.py
phylome2orthologs.py		phylome2orthologs.py
phylome2profile.py		phylome2profile.py
phylome2proteomes.py		phylome2proteomes.py
platanus		platanus
plot.py		plot.py
plot_2d.py		plot_2d.py
plot_heatmap.py		plot_heatmap.py
plot_hist.py		plot_hist.py
plot_hists.py		plot_hists.py
plot_multi.py		plot_multi.py
plot_scatter.py		plot_scatter.py
proteomes2uniprot.py		proteomes2uniprot.py
regex2bed.py		regex2bed.py
remount.sh		remount.sh
remove_old_runs.sh		remove_old_runs.sh
remove_old_snaps		remove_old_snaps
rename_contigs.py		rename_contigs.py
repeats2fasta.py		repeats2fasta.py
repeats2sam.py		repeats2sam.py
romanChr2int.py		romanChr2int.py
runProcess.py		runProcess.py
sam2aligned.py		sam2aligned.py
sam2direct_repeats.py		sam2direct_repeats.py
sam2fastx.py		sam2fastx.py
sam2hist.py		sam2hist.py
sam2indels.py		sam2indels.py
sam2inverted_repeats.py		sam2inverted_repeats.py
sam2mismatches.py		sam2mismatches.py
sam2multiple.py		sam2multiple.py
sam2one_aligned.py		sam2one_aligned.py
sam2spanning.py		sam2spanning.py
sam2split_mapping.bowtie2.py		sam2split_mapping.bowtie2.py
sam2split_mapping.py		sam2split_mapping.py
sam2subset.py		sam2subset.py
sam2unaligned.py		sam2unaligned.py
sam2unique.py		sam2unique.py
samgem2unique.py		samgem2unique.py
samtools2stats.sh		samtools2stats.sh
simulate_heterozygosity.py		simulate_heterozygosity.py
snp2annotate.py		snp2annotate.py
snp2common.py		snp2common.py
snp2plot.py		snp2plot.py
sort.py		sort.py
splitFile.py		splitFile.py
split_files_to_subdirs.awk		split_files_to_subdirs.awk
sqldiff		sqldiff
sqlite3_analyzer		sqlite3_analyzer
sra-accesion2file.py		sra-accesion2file.py
subsample.py		subsample.py
swap.sh		swap.sh
tab2chromosome.py		tab2chromosome.py
tab2rounded.py		tab2rounded.py
tab2synteny.py		tab2synteny.py
taxid2metaphors_proteomes.py		taxid2metaphors_proteomes.py
taxid2phylomedb_proteomes.py		taxid2phylomedb_proteomes.py
taxid2sra.py		taxid2sra.py
template.py		template.py
test.py		test.py
toGFF.py		toGFF.py
to_tape.sh		to_tape.sh
tophat_summary2stats.py		tophat_summary2stats.py
transcript2gene.py		transcript2gene.py
transcript2genename.py		transcript2genename.py
transcript2genomic.py		transcript2genomic.py
tsv2combined.py		tsv2combined.py
tsv2correlation.py		tsv2correlation.py
tsv2kmeans.py		tsv2kmeans.py
twoBitToFa		twoBitToFa
uniprot_fasta2gene_species.py		uniprot_fasta2gene_species.py
updatePhylomeDBStats.py		updatePhylomeDBStats.py
update_spotify.sh		update_spotify.sh
usearch		usearch
usearch10		usearch10
usearch7		usearch7
vcf2common.py		vcf2common.py
vcf2fasta.py		vcf2fasta.py
vcf2heterozygous.py		vcf2heterozygous.py
vcf2snp.py		vcf2snp.py
vcf2snp.ref.py		vcf2snp.ref.py
vcfutils.pl		vcfutils.pl
venn.py		venn.py
video_stabilizer		video_stabilizer
woeusb		woeusb
xls2tex.py		xls2tex.py
xlsx2tsv.py		xlsx2tsv.py
youtube-dl		youtube-dl

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