AGP Utilities

RagTag Version: v1.1.1

The NCBI AGP file specification outlines a standard file format for building sequences ("objects") from a collection of constituent ("component") sequences. RagTag writes all of its assembly manipulation results in this AGP format. Since these files are an essential component of assembly analysis with RagTag, RagTag offers multiple AGP related utilities.

agp2fasta

This utility builds sequence objects in FASTA format given an AGP file and components in FASTA format.

Usage

usage: ragtag.py agp2fasta <scaffolds.agp> <components.fasta>

Build sequences in FASTA format from an AGP v2.1 file.

positional arguments:
  <scaffolds.agp>     AGP v2.1 file
  <components.fasta>  component FASTA file (can be uncompressed or bgzipped)

optional arguments:
  -h, --help          show this help message and exit

agpcheck

This utility checks that the provided AGP files are properly formatted. While agpcheck performs the majority of necessary checks, one should additionally use the NCBI AGP validation tool for a comprehensive validation.

Usage

usage: ragtag.py agpcheck <asm1.agp> [<asm2.agp> ... <asmN.agp>]

Check AGP v2.1 files for validity.

positional arguments:
  <asm1.agp> [<asm2.agp> ... <asmN.agp>]
                        AGP v2.1 files

optional arguments:
  -h, --help            show this help message and exit

If the file is invalid, an error message will be provided. Please see the AGP specification to interpret the error messages.