Genome Assembly Python Packages

camsa

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

ragtag

Tools for fast and flexible genome assembly scaffolding and improvement

pyfastg

A minimal Python library for parsing FASTG files

liftassess

Python tool for assessing genomic coordinate liftOver results using exact alignment geometry, UCSC comparative evidence, reverse liftOver and flanking-context checks, and provenance-aware interpretation.

biomcp-server

🧬 BioMCP — bioinformatics MCP server: 83 tools · 43 databases · PubMed/NCBI/BLAST/PDB/UniProt/enrichment · `pip install biomcp-server` · 生信 MCP 服务器

helen

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

teloclip

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

rsidbuildtranslator

A tool for adding genomic IDs - rsIDS, or chromosome and positions from GRCh37 or GRCh38

instagraal

Large genome reassembly based on Hi-C data, continuation of GRAAL

chromdetect

Detect chromosome-level scaffolds in genome assemblies with inconsistent naming conventions

cobra-meta

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

pypangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

metagenomescope

Visualization tool for (meta)genome assembly graphs

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

makura

NCBI Genome downloader