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cyvcf2
cython + htslib == fast VCF and BCF processingvcfanno
annotate a VCF with other VCFs/BEDs/tabixed filesgoleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binaryslivar
genetic variant expressions, annotation, and filtering for great good.smoove
structural variant calling and genotyping with existing tools, but, smoothly.bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"hts-nim
nim wrapper for htslib for parsing genomics data filescruzdb
python access to UCSC genomes databasepeddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCFbwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genomejigv
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"echtvar
using all the bits for echt rapid variant annotation and filteringcombat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.intintmap
fast int64-int64 map for goduphold
don't get DUP'ed or DEL'ed by your putative SVs.slurmpy
submit jobs to slurm with quick-and-dirty pythonpyfasta
fast, memory-efficient, pythonic (and command-line) access to fasta sequence filesvcfgo
a golang library to read, write and manipulate files in the variant call format.fishers_exact_test
Fishers Exact Test for Python (Cython)xopen
open files for buffered reading and writing in #golanginterlap
fast, pure-python interval overlap testingseqcover
seqcover allows users to view coverage for hundreds of genes and dozens of samplesrare-disease-wf
(WIP) best-practices workflow for rare diseasehts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)go-chartjs
golang library to make https://chartjs.org/ plots (this is vanilla #golang, not gopherjs)hts-nim-tools
useful command-line tools written to showcase hts-nimirelate
Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golangbsub
python wrapper to submit jobs to bsub (and later qsub)combined-pvalues
combining p-values using modified stouffer-liptak for spatially correlated results (probes)align
sequence alignment. global, local, glocal.bigly
a pileup library that embraces the hugeindelope
find large indels (in the blind spot between GATK/freebayes and SV callers)tiwih
simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.cigar
simple library for dealing with SAM cigar stringsgsort
sort genomic data450k-analysis-guide
A Practical (And Opinionated) Guide To Analyzing 450K Datageneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.quicksect
a cythonized, extended version of the interval search tree in bxpoverlap
significance testing over interval overlapsfastbit-python
pythonic access to fastbitnim-lapper
fast easy interval overlapping for nim-langlua-stringy
fast lua string operationspybloomfaster
fast bloomfiltervcfassoc
perform genotype-phenotype-association tests on a VCF with logistic regression.toolshed
python stuff I usebw-python
python wrapper to dpryan79's bigwig library using cffimethylcode
Alignment and Tabulation of BiSulfite Treated Readstnsv
add true-negative SVs from a population callset to a truth-set.hileup
horizontal pileupnim-kmer
DNA kmer operations for nimgenoiser
use the noisebigwig-nim
command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwigvcf-bench
evaluating vcf parsing librariesagoodle
numpy + GDAL == agoodlehts-zig
ziglang + htslibaclust
streaming, flexible agglomerative clusteringgobio
miscellaneous script-like stuff in go for bioinformaticsexcord
extract SV signal from a BAMfastahack-python
cython wrapper to fastahackspacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.bwa-mips
Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profitgobe
a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.bix
tabix file access with golang using biogo machinerysveval
run multiple sv evalution toolsclinical-components
Summarize the clinical (or lab) components and correlations of your dataset.bowfast
run bowtie then bfast on colorspace reads.inheritance
inheritance models for mendelian diseasesskidmarks
find runs (non-randomness) in sequencesfalas
Fragment-Aware Local Assembly for Short-readsbamject
DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.bpbio
basepair bio: a single binary with many useful genomics subtools.kexpr-nim
nim wrapper for Heng Li's kexpr math expression evaluator libraryclustermodel
fitting models to clustered correlated datago-blosc
go wrapper for blosc (blocked number compression with fast random access)celltypes450
adjust for cell-type composition in 450K data using houseman's and other methods.crystal
find clusters and model correlated data from DNA methylation and other genomic sources.variantkey-nim
nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64pedfile
pedigree file parsing and relatedness calculations for nimshuffler
shuffle genome regions to determine probability of user-defined metricgo-giggle
golang wrapper to gigglebedder-rs
an API for intersections of genomic datanim-gzfile
simple reader and writer for gzipped (and regular) filesfind_cns
find conserved non-coding sequences (CNS)nim-cgranges
nim wrapper for https://github.com/lh3/cgranges for faster interval treed4-nim
nim-lang wrapper for https://github.com/38/d4-formatflatfeature
python module for dealing with BED format for genomic data as a numpy array.faidx
faidx for golangtabix-py
interface to tabix using cffi4bit
4bit fasta format.ksw2-nim
nim wrapper for lhs/ksw2 for fast smith-watermanhtsuse
some C stuff that uses htslibnim-minizip
nothing to see here.pyfastx
unified access to fasta, fastx using kseq.h + ??learnflash
all the stuff i want to remember how to do in haxe / flashififo
ififo provides a fast, sized, generic thread-safe FIFO in golang.dotfiles
my .bash, .vim, .* filescysolar
copy of pysolar using cythoncgotbx
yeah, another tabix wrapper for go.totable
simple python / cython wrapper to tokyo cabinet tablesLove Open Source and this site? Check out how you can help us