Genome Analysis Python Packages

bioutils

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

77K 25 21

biocommons-seqrepo

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

67K 52 36

hgvs

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

53K 294 101

cpg-workflows

Genomics workflows for CPG using Hail Batch

5K 12 2

dajin2

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

4K 14 0

nolzss

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

2K 2 0

seqrepo

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

585 52 36

plastburstalign

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

543 1 1

pyani-plus

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

503 36 3

nanorepeat

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

410 20 3

doublehelix

Genomic data manipulation tool

380 6 1

codonu

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

324 28 1

cogclassifier

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

317 85 6

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

307 8 2

helen

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

300 73 12

intervene

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

237 151 30

biocommons-anyvar

Lightweight, portable variation registration and retrieval

156 17 6

anyvar

Lightweight, portable variation registration and retrieval

134 17 6

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

99 6 6

genomehouse

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

94 0 0

maxatac

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

77 30 12

wigman

Generate heatmap plots from genomic BigWig data

60 2 0

makegms

Genome mappability estimation tool

0 0 0