Genome Analysis Python Packages

bioutils

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

94K 25 20

biocommons-seqrepo

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

86K 50 36

hgvs

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

76K 287 97

dajin2

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

6K 14 0

cpg-workflows

Genomics workflows for CPG using Hail Batch

6K 12 2

nolzss

Non-overlapping Lempel–Ziv–Storer–Szymanski Factorization Python Library

2K 2 0

plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across hundreds of plastid genomes using associative arrays

2K 1 0

cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

1K 83 6

pyani-plus

Development repo for pyani-plus (the next iteration of pyani)

774 33 2

seqrepo

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

746 50 36

doublehelix

Genomic data manipulation tool

704 6 0

nanorepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

699 19 4

codonu

An integrated package for codon usage analysis

606 25 1

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

549 73 12

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

445 7 2

intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

433 147 32

biocommons-anyvar

Lightweight, portable variation registration and retrieval

277 16 6

anyvar

AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation standards.

260 16 6

maxatac

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

136 30 11

wigman

Generate heatmap plots from genomic BigWig data

128 2 0

genomehouse

Modular bioinformatics toolkit for sequence analysis, genomic data parsing, machine learning, and visualization all in one package.

118 0 0

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

114 6 6

makegms

Genome mappability estimation tool

45 0 0