Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.

ABSTRACT:

Motivation

With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.

Results

We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allo

SUBMITTER: Formenti G 

PROVIDER: S-EPMC9438950 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature