brentp/goleft

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Language
Go
License
MIT License
Created about 8 years ago
Updated about 2 years ago

brentp/goleft

brentp

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

goleft

goleft is a collection of bioinformatics tools written in go distributed together as a single binary under a liberal (MIT) license.

Running the binary goleft will give a list of subcommands with a short description. Running any subcommand without arguments will give a full help for that command.

Installation

The easiest way to install goleft is to download the latest binary from the releases and make sure to chmod +x the resulting binary.

If you are using go, you can build from source with:

go get -u github.com/brentp/goleft/...
go install github.com/brentp/goleft/cmd/goleft

goleft is also available in bioconda

Commands

covstats : estimate coverage and insert-size statistics on bams by sampling
depth : parallelize calls to samtools in user-defined windows
depthwed : matricize output from depth to n-sites * n-samples
indexcov : quick coverage estimate using only the bam index
indexsplit : generate regions of even data across a cohort (for parallelization)
samplename: report samplename(s) from a bam's SM tag

cyvcf2

cython + htslib == fast VCF and BCF processing

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

slivar

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 files

cruzdb

python access to UCSC genomes database

peddy

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

Jupyter Notebook

bwa-meth

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

jigv

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 filtering

combat.py

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

intintmap

fast int64-int64 map for go

duphold

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

slurmpy

submit jobs to slurm with quick-and-dirty python

pyfasta

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

vcfgo

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 #golang

interlap

fast, pure-python interval overlap testing

seqcover

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

rare-disease-wf

(WIP) best-practices workflow for rare disease

hts-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-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)

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 huge

indelope

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 strings

gsort

sort genomic data

450k-analysis-guide

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

geneimpacts

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

quicksect

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

poverlap

significance testing over interval overlaps

fastbit-python

pythonic access to fastbit

nim-lapper

fast easy interval overlapping for nim-lang

lua-stringy

fast lua string operations

pybloomfaster

fast bloomfilter

vcfassoc

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

toolshed

python stuff I use

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.

hileup

horizontal pileup

nim-kmer

DNA kmer operations for nim

genoiser

bigwig-nim

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

vcf-bench

evaluating vcf parsing libraries

agoodle

numpy + GDAL == agoodle

hts-zig

ziglang + htslib

aclust

streaming, flexible agglomerative clustering

gobio

miscellaneous script-like stuff in go for bioinformatics

excord

extract SV signal from a BAM

fastahack-python

cython wrapper to fastahack

spacepile

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, ..., profit

gobe

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

bix

tabix file access with golang using biogo machinery

sveval

run multiple sv evalution tools

clinical-components

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

bowfast

run bowtie then bfast on colorspace reads.

bcf

bcf parsing in golang

inheritance

inheritance models for mendelian diseases

skidmarks

find runs (non-randomness) in sequences

falas

Fragment-Aware Local Assembly for Short-reads

bamject

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 library

clustermodel

fitting models to clustered correlated data

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.

variantkey-nim

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

pedfile

pedigree file parsing and relatedness calculations for nim

shuffler

shuffle genome regions to determine probability of user-defined metric

go-giggle

golang wrapper to giggle

bedder-rs

an API for intersections of genomic data

nim-gzfile

simple reader and writer for gzipped (and regular) files

find_cns

find conserved non-coding sequences (CNS)

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

flatfeature

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

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

cysolar

copy of pysolar using cython

cgotbx

yeah, another tabix wrapper for go.

totable

simple python / cython wrapper to tokyo cabinet tables