24 projects
streampile
Forward-only pileups streamed from coordinate-sorted SAM, BAM, and CRAM records.
typeline
Write dataclasses to delimited text formats and read them back again.
bedspec
An HTS-specs compliant BED toolkit.
pybgzf
Streaming BGZF compression with on-the-fly tabix and CSI indexing.
cellme
Convert a human cell line identifier into a truth-track VCF of its known mutations.
multiqc-pivot
A MultiQC plugin that folds related samples into one General Statistics row per group with labelled metric columns.
fgpyo
Python bioinformatics and genomics library
qualrepair
Update the FASTQ quality scores from a subsequence FASTQ.
pybedlite
Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)
syncup
Synchronizers for lazy iterators.
prymer
Python primer design library
tp53
Python tools for programmatically annotating VCFs with the Seshat TP53 database.
caseless
A typed dictionary in Python with case-insensitive keys
pyfgaws
Tools and python libraries for working with AWS.
sample-sheet
An Illumina Sample Sheet parsing library
seattle-food-truck
Python client for the glorious food trucks in Seattle
monoclparse
Parse Monocl Excel business report documents and intersect them!
snakescale
Non-strict wrappers for the data pipelining language Snakemake.
pendant
Python 3.6+ library for submitting to AWS Batch interactively.
reticle
Python 3.6+ library for submitting to AWS Batch interactively.
krakenplot
Plot the summary output from Kraken.
nucleic
A Python 3.6 library for plotting mutational spectra.
mpl_helpers
A Python 3.6 library for tweaking matplotlib figures.
refgene_parser
Quickly parse genes and exons from a RefGene file
