Genome Analysis Python Packages

bioutils

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

83K 25 20

biocommons-seqrepo

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

74K 52 36

hgvs

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

65K 291 98

cpg-workflows

Genomics workflows for CPG using Hail Batch

4K 12 2

dajin2

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

3K 14 0

nolzss

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

2K 2 0

cogclassifier

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

1K 85 6

pyani-plus

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

1K 35 3

plastburstalign

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

1K 1 1

seqrepo

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

878 52 36

nanorepeat

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

542 20 4

helen

RNN based assembly HELEN. It works paired with MarginPolish.

491 73 12

codonu

A python project for analysis of codon usage for gene or genome analysis

475 27 1

doublehelix

Genomic data manipulation tool

455 6 1

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

451 8 2

intervene

A tool for intersection and visualization of multiple gene or genomic region sets

438 147 32

biocommons-anyvar

Lightweight, portable variation registration and retrieval

335 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.

266 16 6

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

247 6 6

genomehouse

Modular bioinformatics toolkit for sequence analysis, parsing, ML, and visualization.

179 0 0

maxatac

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

171 30 11

wigman

Generate heatmap plots from genomic BigWig data

112 2 0

makegms

Genome mappability estimation tool

72 0 0