Genome Analysis Python Packages

bioutils

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

89K 25 20

biocommons-seqrepo

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

80K 50 36

hgvs

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

72K 287 97

dajin2

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

5K 14 0

cpg-workflows

CPG workflows for Hail Batch

5K 12 2

nolzss

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

4K 2 0

plastburstalign

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

1K 1 0

seqrepo

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

985 50 36

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

788 7 2

helen

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

723 73 12

pyani-plus

pyANI-plus is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity and similar methods.

685 32 2

nanorepeat

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

631 19 4

doublehelix

Genomic data manipulation tool

587 6 0

cogclassifier

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

557 83 6

intervene

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

529 147 32

codonu

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

515 25 1

anyvar

Lightweight, portable variation registration and retrieval

501 16 6

biocommons-anyvar

Lightweight, portable variation registration and retrieval

222 16 6

genomehouse

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

134 0 0

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

123 6 6

maxatac

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

119 29 11

wigman

Generate heatmap plots from genomic BigWig data

105 2 0

makegms

Genome mappability estimation tool

70 0 0