Sequencing Python Packages

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

galaxy-util

Data intensive science for everyone.

galaxy-tool-util

Data intensive science for everyone.

arda-mapper

High-throughput mapping and domain partitioning of antigen receptor sequences

galaxy-tool-util-models

Data intensive science for everyone.

mirpy-lib

Machine learning for Immune Repertoires

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.

galaxy-objectstore

Data intensive science for everyone.

spacr

spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)

galaxy-job-metrics

Data intensive science for everyone.

pyfastaq

Python3 scripts to manipulate FASTA and FASTQ files

truvari

Structural variant toolkit for VCFs

insilicoseq

:rocket: A sequencing simulator

pybcf

BCF reader

galaxy-containers

Data intensive science for everyone.

galaxy-data

Data intensive science for everyone.

galaxy-app

Data intensive science for everyone.

galaxy-job-execution

Data intensive science for everyone.

galaxy-files

Data intensive science for everyone.

pvactools

A cancer immunotherapy tools suite

checkqc

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

galaxy-config

Data intensive science for everyone.