brwnj

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

bcl2fastq

NextSeq specific bcl2fastq2 wrapper.

fastq-multx

Demultiplexes a fastq.

idplot

compare sequences to a shared root reference sequence.

smoove-nf

Nextflow implementation of the smoove workflow and other tools for SV calling and QC

freebayes-nf

a better freebayes-parallel

covdist

simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.

binder

mybinder.org - open testing.

dotfiles

.files, including ~/.osx — sensible hacker defaults for OS X

jigv

igv.js server and automatic configuration to view bam/cram/vcf/bed

relatively

:bar_chart: Plotly abundance figure with absolute and relative abundances across a hierarchy

arq5x.github.io

bpbio

a single binary with many useful genomics subtools.

brwnj

facets-nf

nextflow implementation of the facets data flow.

ggd-recipes

conda recipes for genomic data

github-vscode-theme-iterm

:octocat: GitHub VS Code Theme for iTerm

gtex-gcs-workaround

:rage1:

haplotyper-nf

haplotyper via sentieon after nf-core/sarek mapping

nf-training-advanced

Customer workshop materials

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

samplot

Plot structural variant signals from many BAMs and CRAMs

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

sentieon-dnaseq-nf

Run DNAseq on Sarek result files

seqcover-nf

quality control sample coverage across genes

slivar

variant expressions, annotation, and filtering for great good.

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

smoove-wdl

WDL implementation of the smoove workflow

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs

somalier-wdl

somalier runner