Pinned Repositories
seqcover
seqcover allows users to view coverage for hundreds of genes and dozens of samples
bcl2fastq
NextSeq specific bcl2fastq2 wrapper.
covdist
simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.
covviz
Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
fastq-join
Squared distance for anchored alignment joiner of ea-utils.
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
umitools
Tools to handle reads sequenced with unique molecular identifiers (UMIs).
bedqc
BED QC tool (in the making)
brwnj's Repositories
brwnj/covviz
Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
brwnj/bcl2fastq
NextSeq specific bcl2fastq2 wrapper.
brwnj/fastq-multx
Demultiplexes a fastq.
brwnj/idplot
compare sequences to a shared root reference sequence.
brwnj/smoove-nf
Nextflow implementation of the smoove workflow and other tools for SV calling and QC
brwnj/freebayes-nf
a better freebayes-parallel
brwnj/covdist
simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.
brwnj/binder
mybinder.org - open testing.
brwnj/dotfiles
.files, including ~/.osx — sensible hacker defaults for OS X
brwnj/jigv
igv.js server and automatic configuration to view bam/cram/vcf/bed
brwnj/relatively
:bar_chart: Plotly abundance figure with absolute and relative abundances across a hierarchy
brwnj/arq5x.github.io
brwnj/bpbio
a single binary with many useful genomics subtools.
brwnj/brwnj
brwnj/facets-nf
nextflow implementation of the facets data flow.
brwnj/ggd-recipes
conda recipes for genomic data
brwnj/github-vscode-theme-iterm
:octocat: GitHub VS Code Theme for iTerm
brwnj/gtex-gcs-workaround
:rage1:
brwnj/haplotyper-nf
haplotyper via sentieon after nf-core/sarek mapping
brwnj/nf-training-advanced
Customer workshop materials
brwnj/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
brwnj/samplot
Plot structural variant signals from many BAMs and CRAMs
brwnj/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
brwnj/sentieon-dnaseq-nf
Run DNAseq on Sarek result files
brwnj/seqcover-nf
quality control sample coverage across genes
brwnj/slivar
variant expressions, annotation, and filtering for great good.
brwnj/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
brwnj/smoove-wdl
WDL implementation of the smoove workflow
brwnj/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs
brwnj/somalier-wdl
somalier runner