My bioinfo toolbox
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python_modules
teaching encode_fetch.py Feb 1, 2017
#fastq2kmers.py# fasta2diverged.py error corrected Apr 16, 2015
.gitignore Initial commit Feb 25, 2015
BRH.py brh.py based on blat added Apr 11, 2016
FastaIndex.py solaris May 10, 2018
LICENCE.txt licence added Aug 20, 2014
README moved to github Feb 25, 2015
README.md moved to github Feb 25, 2015
SOLiD2Std.pl SOLiD2Std.pl added from http://seqanswers.com/forums/showthread.php?t… May 8, 2015
SraTailor moved to github Feb 25, 2015
TE_analysis.py
a.out
abi2fastq.py neptune sync Feb 22, 2014
annotated_chromosomes.py fastq2array.py snap Oct 20, 2016
augustus_gff2fasta.py fastq2array.py snap Oct 20, 2016
bam2RNAediting.py fastq2array.py snap Oct 20, 2016
bam2amplicons.py fastq2array.py snap Oct 20, 2016
bam2bigwig.py
bam2cnv.py fastq2fasta.py chunksize=1 Nov 29, 2016
bam2counts.py fastq2array.py snap Oct 20, 2016
bam2cov.py fastq2array.py snap Oct 20, 2016
bam2cov.py_bck fasta2diverged.py error corrected Apr 16, 2015
bam2cov_multi_pool.py fastq2array.py snap Oct 20, 2016
bam2cov_pool.py fastq2array.py snap Oct 20, 2016
bam2coverage.py re-freshed bin Dec 4, 2013
bam2difference.py
bam2editing_penetrance.py fastq2array.py snap Oct 20, 2016
bam2enhancers.py fastq2array.py snap Oct 20, 2016
bam2heterozygous.py heterozygous2fasta.py Apr 13, 2017
bam2mitochondrial.py
bam2paternal.py fastq2array.py snap Oct 20, 2016
bam2ploidy.py bam2ploidy.py May 12, 2018
bam2snps.py bam2snps.py Oct 27, 2015
bam2snps.ref.py bam2snps.ref.py Sep 22, 2018
bam2stranded.py re-freshed bin Dec 4, 2013
bam2sv.py fastq2array.py snap Oct 20, 2016
bam2vcf.py re-freshed bin Dec 4, 2013
barcode2fqname.py barcode2fqname.py Jan 13, 2018
bed2RNALfold.py fastq2array.py snap Oct 20, 2016
bed2cnv.py fastq2array.py snap Oct 20, 2016
bed2cnv_plot.py
bed2count_filter.py fastq2array.py snap Oct 20, 2016
bed2graph.py fastq2array.py snap Oct 20, 2016
bed2igv_batch.py fastq2array.py snap Oct 20, 2016
bed2region.py regex2bed.py add-ons Sep 10, 2015
bed2stats.py fastq2array.py snap Oct 20, 2016
bedGraphToBigWig
bedcount2plot.py fastq2array.py snap Oct 20, 2016
blast2hits.py exonerate2ptc.py working Mar 31, 2017
blast2matrix.py fastq2array.py snap Oct 20, 2016
blast2nohit.py fastq2array.py snap Oct 20, 2016
blastout2identity.py
blastout2profile.py fastq2array.py snap Oct 20, 2016
blat blat Dec 31, 2014
blat2collapse.py fastq2array.py snap Oct 20, 2016
boxplot.py fastq2array.py snap Oct 20, 2016
brh.py fastq2array.py snap Oct 20, 2016
bwa
combine_windows.py fastq2fasta.py multiprocessing Oct 27, 2016
composer hts Apr 8, 2018
contig2gc.py
coords2ordered.py fastq2array.py snap Oct 20, 2016
counts2cnv.mean.py fastq2array.py snap Oct 20, 2016
counts2cnv.py fastq2array.py snap Oct 20, 2016
coverage_graph.py fastq2array.py snap Oct 20, 2016
coverage_track.py fastq2array.py snap Oct 20, 2016
csv2common.py
csv2fasta.py
csv2xls.py igv2 Aug 9, 2017
cuffdiff2de.py fastq2array.py snap Oct 20, 2016
decypher2bed.py
deseq2annotate.py fastq2array.py snap Oct 20, 2016
deseq2de.py re-freshed bin Dec 4, 2013
dropboxcrg dropboxcrg Dec 2, 2014
duptree
embl2fasta.py fastq2array.py snap Oct 20, 2016
embl2gb.py corrected snp2annotate.py Feb 11, 2014
embl2gff.pl
embl2gtf.py corrected filterReads.new.py Mar 6, 2014
embl2protein.py re-freshed bin Dec 4, 2013
ena_download_and_rename.py ena_download_and_rename.py Jan 13, 2018
exonerate exonerate Apr 29, 2016
exonerate2ptc.py bam2heterozygous.py Apr 10, 2017
exonerategff2gtf.py exonerategff2gtf.py May 6, 2016
fast52reads.py fast52reads.py Aug 1, 2018
fasta2GC.py fastq2array.py snap Oct 20, 2016
fasta2GCplot.py fastq2array.py snap Oct 20, 2016
fasta2agp.py fastq2array.py snap Oct 20, 2016
fasta2clusters.py
fasta2concatenated.py
fasta2contigs.py fastq2array.py snap Oct 20, 2016
fasta2diverged.py modifications2rna.py Nov 30, 2017
fasta2gaps.py fastq2array.py snap Oct 20, 2016
fasta2gc.py fasta2gc Oct 19, 2015
fasta2homozygous.py fastq2array.py snap Oct 20, 2016
fasta2loh.py
fasta2softmasked.py
fasta_stats.py encode_fetch.py Feb 1, 2017
fastq2fasta.py fastq2fasta.py Nov 22, 2017
fastq2fastq.py corrected snp2annotate.py Feb 11, 2014
fastq2kmers.py fastq2array.py snap Oct 20, 2016
fastq2random.py fastq2array.py snap Oct 20, 2016
fastq2repeats.py fastq2array.py snap Oct 20, 2016
fastq2shuffledFastQ.py re-freshed bin Dec 4, 2013
fastq2shuffledFasta.py re-freshed bin Dec 4, 2013
fastq2sspace.bwamem.py fastq2array.py snap Oct 20, 2016
fastq2sspace.py
fastq2sspace_bwamem.py fastq2array.py snap Oct 20, 2016
fastq2telomers.py
fastq2trim.py fastq2array.py snap Oct 20, 2016
fastq_select.py fastq2array.py snap Oct 20, 2016
fastx2reverse_complement.py FastaIndex.py Sep 12, 2016
filterReads.new.py filterReads.new.py single-end mode solved problem Mar 10, 2017
filterReads.py filterReads.py Feb 7, 2018
filter_by_coverage.py fastq2array.py snap Oct 20, 2016
filter_fasta.py fastq2array.py snap Oct 20, 2016
find_telomers.py find_telomers.py with gzip support Aug 20, 2015
fluxgtf2counts.py fastq2array.py snap Oct 20, 2016
fpkm2expression_plot.py modifications2rna.py Nov 30, 2017
fpkm2major.py fastq2array.py snap Oct 20, 2016
fqextract fqextract added Mar 21, 2015
fqextract.c fasta2diverged.py error corrected Apr 16, 2015
fqextract.py bam2cov.py Mar 30, 2015
fqextract_not.py bam2cov.py Mar 30, 2015
gb2embl.py corrected snp2annotate.py Feb 11, 2014
gb2fasta.py fastq2array.py snap Oct 20, 2016
gb2gtf.py usearch Jun 12, 2017
gb2protein.py
gem.py re-freshed bin Dec 4, 2013
genbank2fasta.py
gene2go.py re-freshed bin Dec 4, 2013
gene2selected.py fastq2array.py snap Oct 20, 2016
genePredToGtf genePredToGtf Feb 2, 2015
geneid2genename.py fastq2array.py snap Oct 20, 2016
genemark2bed.py
genemark2bedGraph.py re-freshed bin Dec 4, 2013
genome_graph.py
genome_track.py fastq2array.py snap Oct 20, 2016
get_complete_genomes.NCBI.py exonerate2ptc.py working Mar 31, 2017
get_fragmented_assemblies.py Merge branch 'master' of ssh://bitbucket.org/lpryszcz/bin Oct 26, 2014
gff2bed.py fast52reads.py Aug 1, 2018
grep.py grep.py with -s Jul 18, 2017
gtf2bed.py
gtf2bed_transcripts.py gtf2bed_transcripts Nov 16, 2015
gtf2embl.py
gtf2fasta.py re-freshed bin Dec 4, 2013
heterozygous2fasta.py heterozygous2fasta.py Apr 19, 2017
hibernate.sh Merge branch 'master' of bitbucket.org:lpryszcz/bin Aug 27, 2014
idxstats2copynumber.py fastq2array.py snap Oct 20, 2016
idxstats2coverage.py re-freshed bin Dec 4, 2013
idxstats2species.py re-freshed bin Dec 4, 2013
igv2 modifications2rna.py Nov 30, 2017
insertSize.py re-freshed bin Dec 4, 2013
insert_estimation.py re-freshed bin Dec 4, 2013
insert_size_plot.py fastq2random.py Oct 13, 2014
interpro_tsv2function.py interpro_tsv2*.py reporting also annotated fasta Feb 8, 2017
interpro_tsv2go.py interpro_tsv2*.py Feb 8, 2017
intersect2bed.py regex2bed.py add-ons Sep 10, 2015
isoforms2longest.py re-freshed bin Dec 4, 2013
khash.h fasta2diverged.py error corrected Apr 16, 2015
kmc kmc added Aug 20, 2015
kmc_dump kmc added Aug 20, 2015
latexencode.py
liftOver added liftOver Feb 26, 2015
local_assembly.py fastq2array.py snap Oct 20, 2016
local_assembly.simple.bowtie2.py fastq2array.py snap Oct 20, 2016
local_assembly.simple.bwamem.py fastq2array.py snap Oct 20, 2016
local_assembly.simple.py fastq2array.py snap Oct 20, 2016
loh2chrom.py moved to github Feb 25, 2015
lsfd.sh moved to github Feb 25, 2015
memusage.sh memusage Sep 6, 2016
modifications2rna.py modifications2signatures.py Dec 1, 2017
modifications2signatures.py bam2ploidy.py Dec 13, 2017
mpileup2baf.pl bam2sv.py isize > .05 and < .95 Mar 17, 2014
n50.py n50 added Aug 11, 2015
newick2rooted.py taxonomy.py updated Aug 14, 2014
nextseq.py
nextseq.sh
nucmer2ordered.py fastq2array.py snap Oct 20, 2016
nw2species.py re-freshed bin Dec 4, 2013
oslay neptune branch Oct 26, 2014
pbsim pbsim Sep 6, 2016
pbsim.model_qc_ccs pbsim Sep 6, 2016
pbsim.model_qc_clr pbsim Sep 6, 2016
pfam2gtf.py
phylome2nSizeFamilies.py fastq2array.py snap Oct 20, 2016
phylome2orthologous_groups.py fastq2array.py snap Oct 20, 2016
phylome2orthologs.py fastq2array.py snap Oct 20, 2016
phylome2profile.py
phylome2proteomes.py fastq2array.py snap Oct 20, 2016
platanus
plot.py fastq2array.py snap Oct 20, 2016
plot_2d.py fastq2array.py snap Oct 20, 2016
plot_heatmap.py fastq2array.py snap Oct 20, 2016
plot_hist.py fastq2array.py snap Oct 20, 2016
plot_multi.py fastq2array.py snap Oct 20, 2016
proteomes2uniprot.py fastq2array.py snap Oct 20, 2016
redundans.py
regex2bed.py fastq2array.py snap Oct 20, 2016
remount.sh moved to github Feb 25, 2015
rename_contigs.py rename_fasta Jan 8, 2016
repeats2fasta.py fastq2array.py snap Oct 20, 2016
repeats2sam.py fastq2array.py snap Oct 20, 2016
runProcess.py re-freshed bin Dec 4, 2013
sam2aligned.py re-freshed bin Dec 4, 2013
sam2direct_repeats.py sam2direct_repeats.py Jul 23, 2015
sam2fastx.py fastq2array.py snap Oct 20, 2016
sam2hist.py fastq2array.py snap Oct 20, 2016
sam2indels.py fastq2array.py snap Oct 20, 2016
sam2inverted_repeats.py
sam2mismatches.py fastq2array.py snap Oct 20, 2016
sam2multiple.py fastq2array.py snap Oct 20, 2016
sam2one_aligned.py fastq2array.py snap Oct 20, 2016
sam2spanning.py
sam2split_mapping.bowtie2.py
sam2split_mapping.py fastq2array.py snap Oct 20, 2016
sam2unaligned.py fastq2array.py snap Oct 20, 2016
sam2unique.py re-freshed bin Dec 4, 2013
samgem2unique.py re-freshed bin Dec 4, 2013
simulate_heterozygosity.py fastq2array.py snap Oct 20, 2016
snp2annotate.py fastq2array.py snap Oct 20, 2016
snp2common.py bit Sep 22, 2018
snp2plot.py fastq2array.py snap Oct 20, 2016
sort.py
splitFile.py fastq2array.py snap Oct 20, 2016
sra-accesion2file.py fastq2array.py snap Oct 20, 2016
swap.sh swap.sh Mar 9, 2017
tab2chromosome.py bam2cnv.py Nov 4, 2016
tab2rounded.py grep.py peyote2 Jul 18, 2017
tab2synteny.py
taxid2metaphors_proteomes.py fastq2array.py snap Oct 20, 2016
taxid2phylomedb_proteomes.py fastq2array.py snap Oct 20, 2016
taxid2sra.py
template.py fastq2array.py snap Oct 20, 2016
test.py bam2snps.py Oct 27, 2015
toGFF.py neptune sync Feb 22, 2014
tophat_summary2stats.py bam2snps.ref.py mpileup options Apr 25, 2014
transcript2gene.py
transcript2genename.py
transcript2genomic.py
tsv2combined.py
tsv2correlation.py fastq2array.py snap Oct 20, 2016
tsv2kmeans.py fastq2array.py snap Oct 20, 2016
twoBitToFa twoBitToFa Apr 14, 2016
updatePhylomeDBStats.py fastq2array.py snap Oct 20, 2016
usearch usearch Jun 12, 2017
usearch10 usearch Jun 12, 2017
usearch7 usearch Jun 12, 2017
vcf2common.py fastq2array.py snap Oct 20, 2016
vcf2fasta.py fastq2array.py snap Oct 20, 2016
vcf2heterozygous.py fastq2array.py snap Oct 20, 2016
vcf2snp.py re-freshed bin Dec 4, 2013
vcf2snp.ref.py re-freshed bin Dec 4, 2013
vcfutils.pl re-freshed bin Dec 4, 2013
venn.py venn.py yoga3 ok May 18, 2016
video_stabilizer moved to github Feb 25, 2015
xls2tex.py
xlsx2tsv.py xlsx2tsv.py Jan 8, 2016

README.md

BIOINFORMATICS BINARIES

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