Discover brentp/bowfast Open Source project

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Created about 13 years ago
Updated about 12 years ago

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run bowtie then bfast on colorspace reads.

cyvcf2

cython + htslib == fast VCF and BCF processing

Cython

366

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

332

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

202

slivar

genetic variant expressions, annotation, and filtering for great good.

Nim

189

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

187

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

181

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Nim

180

hts-nim

nim wrapper for htslib for parsing genomics data files

Nim

149

cruzdb

python access to UCSC genomes database

Python

129

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Jupyter Notebook

122

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

Python

116

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Nim

107

echtvar

using all the bits for echt rapid variant annotation and filtering

Rust

105

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

Python

intintmap

fast int64-int64 map for go

duphold

don't get DUP'ed or DEL'ed by your putative SVs.

Nim

slurmpy

submit jobs to slurm with quick-and-dirty python

Python

pyfasta

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

Python

vcfgo

a golang library to read, write and manipulate files in the variant call format.

fishers_exact_test

Fishers Exact Test for Python (Cython)

Python

xopen

open files for buffered reading and writing in #golang

interlap

fast, pure-python interval overlap testing

Python

seqcover

seqcover allows users to view coverage for hundreds of genes and dozens of samples

Nim

rare-disease-wf

(WIP) best-practices workflow for rare disease

Nextflow

hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

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-nim

Nim

irelate

Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang

bsub

python wrapper to submit jobs to bsub (and later qsub)

Python

combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)

Python

align

sequence alignment. global, local, glocal.

Python

bigly

a pileup library that embraces the huge

indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

Nim

tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

Nim

cigar

simple library for dealing with SAM cigar strings

Python

gsort

sort genomic data

450k-analysis-guide

A Practical (And Opinionated) Guide To Analyzing 450K Data

TeX

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

Python

quicksect

a cythonized, extended version of the interval search tree in bx

Python

poverlap

significance testing over interval overlaps

Python

fastbit-python

pythonic access to fastbit

Python

nim-lapper

fast easy interval overlapping for nim-lang

Nim

lua-stringy

fast lua string operations

pybloomfaster

fast bloomfilter

vcfassoc

perform genotype-phenotype-association tests on a VCF with logistic regression.

Python

toolshed

python stuff I use

Python

bw-python

python wrapper to dpryan79's bigwig library using cffi

methylcode

Alignment and Tabulation of BiSulfite Treated Reads

tnsv

add true-negative SVs from a population callset to a truth-set.

Nim

hileup

horizontal pileup

nim-kmer

DNA kmer operations for nim

Nim

genoiser

use the noise

Nim

bigwig-nim

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

Nim

vcf-bench

evaluating vcf parsing libraries

Zig

agoodle

numpy + GDAL == agoodle

Python

hts-zig

ziglang + htslib

Zig

aclust

streaming, flexible agglomerative clustering

Python

gobio

miscellaneous script-like stuff in go for bioinformatics

excord

extract SV signal from a BAM

fastahack-python

cython wrapper to fastahack

C++

spacepile

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

Rust

bwa-mips

Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit

Python

gobe

a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.

Haxe

bix

tabix file access with golang using biogo machinery

sveval

run multiple sv evalution tools

Python

clinical-components

Summarize the clinical (or lab) components and correlations of your dataset.

Python

bcf

bcf parsing in golang

inheritance

inheritance models for mendelian diseases

Python

skidmarks

find runs (non-randomness) in sequences

Python

falas

Fragment-Aware Local Assembly for Short-reads

Nim

bamject

DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.

Nim

bpbio

basepair bio: a single binary with many useful genomics subtools.

Nim

kexpr-nim

nim wrapper for Heng Li's kexpr math expression evaluator library

clustermodel

fitting models to clustered correlated data

Python

go-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.

Python

variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

pedfile

pedigree file parsing and relatedness calculations for nim

Nim

shuffler

shuffle genome regions to determine probability of user-defined metric

Python

go-giggle

golang wrapper to giggle

bedder-rs

an API for intersections of genomic data

Rust

nim-gzfile

simple reader and writer for gzipped (and regular) files

Nim

find_cns

find conserved non-coding sequences (CNS)

Python

nim-cgranges

nim wrapper for https://github.com/lh3/cgranges for faster interval tree

d4-nim

nim-lang wrapper for https://github.com/38/d4-format

Nim

flatfeature

python module for dealing with BED format for genomic data as a numpy array.

Python

faidx

faidx for golang

tabix-py

interface to tabix using cffi

4bit

4bit fasta format.

ksw2-nim

nim wrapper for lhs/ksw2 for fast smith-waterman

htsuse

some C stuff that uses htslib

nim-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 / flash

ififo

ififo provides a fast, sized, generic thread-safe FIFO in golang.

dotfiles

my .bash, .vim, .* files

Shell

cysolar

copy of pysolar using cython

Python

cgotbx

yeah, another tabix wrapper for go.

100

totable

simple python / cython wrapper to tokyo cabinet tables

brentp/bowfast

brentp

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