agptools

Tools for working with agp files

Full documentation at github pages.

Introduction

The AGP format is a tab-separated table format describing how components of a genome assembly fit together. NCBI accepts assemblies for submission in the format of a fasta file giving the sequences of components (usually contigs) along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. For this reason, scaffolders such as SALSA output this format alongside the fasta file of the scaffolded assembly containing gaps and all.

Unfortunately, scaffolding never really works perfectly, so you invariably have to correct mistakes or add in other sources of data such as synteny with a related species or a phyiscal map to get an assembly to chromosome level. While you could perform this manual curation process by editing the fasta file of scaffolds, I think it is a lot easier to leave the fasta file of contigs intact and move things around in the AGP file. For example, let's say the scaffolder misorients a contig. Fixing this in the fasta would require taking a chunk from the middle of a sequence, reverse orienting it, and pasting it back together. Fixing it in the AGP file is as simple as finding the line corresponding to that contig and changing the character in the orientation column from '+' to '-'.

agptools is a suite of scripts for performing edits to an AGP file during this manual curation stage of genome assembly. It contains modules for operations you might want to perform on an agp file, like splitting a contig or scaffold into multiple pieces, joining various scaffolds together into a superscaffold, reverse-complementing a piece of a scaffold, transforming a bed file from contig into scaffold coordinates, and removing or renaming scaffolds. Each of these use cases is explained in depth in the manual.

Installation

I'll get this on PyPI soon so that you can install this with one command instead of three, but for now, you have to clone the repository first:

git clone https://github.com/esrice/agptools.git
cd agptools
pip install .