brentp

Doing genomics from the Netherlands

University of UtahUtrecht, The Netherlands

Pinned Repositories

bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
Language:C181 16 16104
cyvcf2
cython + htslib == fast VCF and BCF processing
Language:Cython358 7 21171
echtvar
using all the bits for echt rapid variant annotation and filtering
Language:Rust130 4 279
goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Language:Go207 16 6624
hts-nim
nim wrapper for htslib for parsing genomics data files
Language:Nim153 10 5526
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language:Nim660 23 20799
slivar
genetic variant expressions, annotation, and filtering for great good.
Language:Nim242 11 15522
smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Language:Go221 10 22921
somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language:Nim254 11 12235
vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Language:Go348 26 14156

brentp's Repositories

brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language:Nim660 23 20799
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
Language:Cython358 7 21171
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Language:Go348 26 14156
brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language:Nim254 11 12235
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
Language:Nim242 11 15522
brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Language:Go221 10 22921
brentp/goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Language:Go207 16 6624
brentp/hts-nim
nim wrapper for htslib for parsing genomics data files
Language:Nim153 10 5526
brentp/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
Language:Python137 13 7454
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
Language:Rust130 4 279
brentp/jigv
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
Language:Nim121 3 217
brentp/intintmap
fast int64-int64 map for go
Language:Go95 7 618
brentp/fishers_exact_test
Fishers Exact Test for Python (Cython)
Language:Python61 5 3120
brentp/rare-disease-wf
(WIP) best-practices workflow for rare disease
Language:Nextflow56 8 108
brentp/tiwih
simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.
Language:Nim43 3 10
brentp/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
Language:Python32 4 915
brentp/fraguracy
overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
Language:Rust27 2 41
brentp/pbr
drunk on perbase pileups and lua expressions
Language:Rust17 2 82
brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
Language:Rust13 3 2
brentp/xvcf-rs
VCF/BCF [un]compressed [un]indexed
Language:Rust8 2 0
brentp/oodles
oodles of bioinformatics tools
Language:Rust7 2 0
brentp/bedder-rs
an API for intersections of genomic data
Language:Rust4 4 10
brentp/nim-minizip
nothing to see here.
Language:C2 3 0
brentp/fgoxide
Quality of life improvements in Rust.
Language:Rust1 1 0
brentp/perbase
Per-base per-nucleotide depth analysis
Language:Rust1 1 0
brentp/polars-learn
learn rust polars
Language:Rust1 2 0
brentp/bedtools2
A powerful toolset for genome arithmetic.
Language:C++3 0
brentp/fastquorum
nothing to see here
Language:Nextflow1 0
brentp/help-repositories
getting help on stuff.
Language:Rust2 0
brentp/rust-htslib
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
Language:Rust1 0