Description

Utilities to assemble an organelle genome using ABySS.

Dependencies

The following tools must be installed and available on your PATH:

• ABySS
• samtools
• bwa
• bioawk
• bedtools
• R

Tools

• abyss-organelle.mk (main script): do a standard ABySS assembly and then extract organelle scaffolds
• classify.mk: split contigs file into 'organelle' and 'genome' contigs using k-means clustering on coverage, %GC content, and length
• classify.r: R script to do k-means clustering for classify.mk
• cov-hist-to-mean: convert 'bedtools genomecov' output to mean coverage per contig
• fastx2gc: compute %GC content for each seq in a FASTA/FASTQ file
• smartcat: does zcat/bzcat/cat based on file type (thanks to David Bartle)

Usage

The main assembly script is abyss-organelle.mk. Usage of abyss-organelle.mk is the same as abyss-pe (see the ABySS README.md), except that it requires an additional parameter:

• readfiles: a list of FASTA/FASTQ/SAM/BAM to align to the scaffolds in order to determine read coverage during the classification step

Usage example

$ abyss-organelle.mk name=arabidopsis k=50 readfiles='reads1.fa.gz reads2.fa.gz' lib=readfiles

Optional parameters

• classify: specify whether to do the classification at the contig stage or the scaffold stage. Possible values are classify=scaffolds or classify=contigs [classify=scaffolds]
• j: specify number of threads