Pinned Repositories
bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
cyvcf2
cython + htslib == fast VCF and BCF processing
echtvar
using all the bits for echt rapid variant annotation and filtering
goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
hts-nim
nim wrapper for htslib for parsing genomics data files
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
slivar
genetic variant expressions, annotation, and filtering for great good.
smoove
structural variant calling and genotyping with existing tools, but, smoothly.
somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
brentp's Repositories
brentp/cruzdb
python access to UCSC genomes database
brentp/duphold
don't get DUP'ed or DEL'ed by your putative SVs.
brentp/interlap
fast, pure-python interval overlap testing
brentp/hts-nim-tools
useful command-line tools written to showcase hts-nim
brentp/seqcover
seqcover allows users to view coverage for hundreds of genes and dozens of samples
brentp/go-chartjs
golang library to make https://chartjs.org/ plots (this is vanilla #golang, not gopherjs)
brentp/irelate
Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang
brentp/bigly
a pileup library that embraces the huge
brentp/cigar
simple library for dealing with SAM cigar strings
brentp/gsort
sort genomic data
brentp/poverlap
significance testing over interval overlaps
brentp/lua-stringy
fast lua string operations
brentp/bigwig-nim
command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig
brentp/genoiser
use the noise
brentp/kexpr-nim
nim wrapper for Heng Li's kexpr math expression evaluator library
brentp/nim-gzfile
simple reader and writer for gzipped (and regular) files
brentp/pedfile
pedigree file parsing and relatedness calculations for nim
brentp/faidx
faidx for golang
brentp/covviz
Multi-sample genome coverage viewer to observe large, coverage-based anomalies
brentp/crampex
cram reader in golang via system call to samtools
brentp/longSTR
Call STRs in long reads or assembled contigs using TRF
brentp/Nim
Nim is a compiled, garbage-collected systems programming language with a design that focuses on efficiency, expressiveness, and elegance (in the order of priority).
brentp/blosc2-nim
nim language wrapper for the blosc2 compression libray.
brentp/c-blosc2
A simple, compressed, fast and persistent data store library for C
brentp/CaBagE-manuscript
brentp/cqf-nim
nim wrapper for counting quotient filter
brentp/docker-nim-cross
Dockerfile for Nim lang
brentp/exter
coordinate transformation exon-space -> genome-space and back again.
brentp/hts
biogo high throughput sequencing repository
brentp/igv-reports
Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.