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/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
brentp/goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
brentp/hts-nim
nim wrapper for htslib for parsing genomics data files
brentp/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
brentp/jigv
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
brentp/vcfgo
a golang library to read, write and manipulate files in the variant call format.
brentp/fishers_exact_test
Fishers Exact Test for Python (Cython)
brentp/vcfexpress
expressions on VCFs
brentp/rare-disease-wf
(WIP) best-practices workflow for rare disease
brentp/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
brentp/fraguracy
overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
brentp/pbr
drunk on perbase pileups and lua expressions
brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
brentp/xvcf-rs
VCF/BCF [un]compressed [un]indexed
brentp/go-blosc
go wrapper for blosc (blocked number compression with fast random access)
brentp/bedder-rs
an API for intersections of genomic data
brentp/d4-nim
nim-lang wrapper for https://github.com/38/d4-format
brentp/svtyper
Bayesian genotyper for structural variants
brentp/nf-simple
brentp/nim-minizip
nothing to see here.
brentp/fgoxide
Quality of life improvements in Rust.
brentp/perbase
Per-base per-nucleotide depth analysis
brentp/help-repositories
getting help on stuff.
brentp/rust-htslib
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.