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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 == agoodleaclust
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.bcf
bcf parsing in golanginheritance
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