Agptools: a utility suite for editing genome assemblies

Abstract

Summary: The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. For this reason, many scaffolding software pipelines output assemblies in this format. However, although many programs for assembling and scaffolding genomes read and write this format, there is currently no published software for making edits to AGP files when performing assembly curation. We present agptools, a suite of command-line programs that can perform common operations on AGP files, such as breaking and joining sequences, inverting pieces of assembly components, assembling contigs into larger sequences based on an AGP file, and transforming between coordinate systems of different assembly layouts. Additionally, agptools includes an API that writers of other software packages can use to read, write, and manipulate AGP files within their own programs.

Availability and implementation: Source code and binaries freely available for download at https://github.com/WarrenLab/agptools, implemented in Python and supported on all operating systems.

Figure 1.

Subcommands of agptools. (a) The join command joins two or more separate sequences into a single sequence. (b) The split command splits a sequence at a given location into two sequences. (c) The flip command inverts part of a sequence. (d) The assemble command produces an assembled fasta file from a fasta file of sequence components and an AGP file giving their order and orientation. (e) The transform command translates coordinates in a bed file into the coordinate system of assembled sequences.