brentp

Brent Pedersen's repositories

mosdepth

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

Language:NimMIT667 23 209

cyvcf2

cython + htslib == fast VCF and BCF processing

Language:CythonMIT360 7 212

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

Language:GoMIT350 26 141

somalier

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

Language:NimMIT254 10 124

slivar

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

Language:NimMIT246 11 156

goleft

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

Language:GoMIT208 16 66

hts-nim

nim wrapper for htslib for parsing genomics data files

Language:NimMIT154 10 55

bwa-meth

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

Language:PythonMIT139 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:NimMIT122 3 21

intintmap

fast int64-int64 map for go

Language:GoBSD-2-Clause95 7 6

slurmpy

submit jobs to slurm with quick-and-dirty python

Language:PythonMIT92 7 7

vcfgo

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

Language:GoMIT67 8 11

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

hileup

horizontal pileup

Language:CApache-2.016 50

tnsv

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

Language:NimMIT15 30

spacepile

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

Language:RustMIT14 3 2

oodles

oodles of bioinformatics tools

Language:RustMIT7 20

go-blosc

go wrapper for blosc (blocked number compression with fast random access)

Language:GoMIT5 40

polars-learn

learn rust polars

Language:RustMIT1 20

bedtools2

A powerful toolset for genome arithmetic.

Language:C++GPL-2.0030

d4-format

The D4 Quantitative Data Format

Language:RustMIT010

fastquorum

nothing to see here

Language:NextflowMIT010

rust-htslib

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

Language:RustMIT010

rusty_v8

Rust bindings for the V8 JavaScript engine

Language:RustMIT010

sv-channels

Deep learning-based structural variant caller

Language:Jupyter NotebookApache-2.0020

v8rustruct

broken example of rust <=> js so I can get help

Language:RustMIT020