brentp

Brent Pedersen's repositories

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language:NimMIT661 23 207

cyvcf2

cython + htslib == fast VCF and BCF processing

Language:CythonMIT358 7 211

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

Language:GoMIT348 26 141

somalier

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

Language:NimMIT254 11 122

slivar

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

Language:NimMIT242 11 155

smoove

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

Language:GoApache-2.0222 10 229

goleft

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

Language:GoMIT207 16 66

hts-nim

nim wrapper for htslib for parsing genomics data files

Language:NimMIT153 10 55

bwa-meth

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

Language:PythonMIT137 13 74

echtvar

using all the bits for echt rapid variant annotation and filtering

Language:RustMIT130 4 27

jigv

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

Language:NimMIT121 3 21

intintmap

fast int64-int64 map for go

Language:GoBSD-2-Clause95 7 6

fishers_exact_test

Fishers Exact Test for Python (Cython)

Language:PythonBSD-3-Clause61 5 31

rare-disease-wf

(WIP) best-practices workflow for rare disease

Language:NextflowMIT56 8 10

tiwih

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

Language:NimMIT43 3 1

geneimpacts

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

Language:PythonMIT32 4 9

fraguracy

overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites

Language:RustMIT27 2 4

pbr

drunk on perbase pileups and lua expressions

Language:RustMIT17 2 8

spacepile

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

Language:RustMIT13 3 2

xvcf-rs

VCF/BCF [un]compressed [un]indexed

Language:RustMIT8 20

oodles

oodles of bioinformatics tools

Language:RustMIT7 20

bedder-rs

an API for intersections of genomic data

Language:RustMIT4 4 10

nim-minizip

nothing to see here.

Language:C2 30

fgoxide

Quality of life improvements in Rust.

Language:RustMIT1 10

perbase

Per-base per-nucleotide depth analysis

Language:RustMIT1 10

polars-learn

learn rust polars

Language:RustMIT1 20

bedtools2

A powerful toolset for genome arithmetic.

Language:C++GPL-2.0030

fastquorum

nothing to see here

Language:NextflowMIT010

help-repositories

getting help on stuff.

Language:RustMIT020

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

Language:RustMIT010