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/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
brentp/slurmpy
submit jobs to slurm with quick-and-dirty python
brentp/vcfgo
a golang library to read, write and manipulate files in the variant call format.
brentp/xopen
open files for buffered reading and writing in #golang
brentp/bsub
python wrapper to submit jobs to bsub (and later qsub)
brentp/combined-pvalues
combining p-values using modified stouffer-liptak for spatially correlated results (probes)
brentp/nim-lapper
fast easy interval overlapping for nim-lang
brentp/hileup
horizontal pileup
brentp/vcf-bench
evaluating vcf parsing libraries
brentp/tnsv
add true-negative SVs from a population callset to a truth-set.
brentp/hts-zig
ziglang + htslib
brentp/nim-kmer
DNA kmer operations for nim
brentp/sveval
run multiple sv evalution tools
brentp/go-blosc
go wrapper for blosc (blocked number compression with fast random access)
brentp/d4-nim
nim-lang wrapper for https://github.com/38/d4-format
brentp/lumpy-sv
lumpy: a general probabilistic framework for structural variant discovery
brentp/dysgu
dysgu-SV is a collection of tools for calling structural variants using short or long reads
brentp/svpack
Structural variant (SV) analysis tools
brentp/truvari
SVBenchmarkingTool
brentp/alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
brentp/d4-format
The D4 Quantitative Data Format
brentp/libvbyte
A fast implementation for varbyte 32bit/64bit integer compression
brentp/manta
Structural variant and indel caller for mapped sequencing data
brentp/nibsv
SV genotyping with kmers (created during Baylor hackathon)
brentp/paragraph
Graph realignment tools for structural variants
brentp/power
brentp/rusty_v8
Rust bindings for the V8 JavaScript engine
brentp/sv-channels
Deep learning-based structural variant caller
brentp/v8rustruct
broken example of rust <=> js so I can get help
brentp/vbyte-zig
vbyte compression for zig using https://github.com/cruppstahl/libvbyte