sort-contigs 0.2.2

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sort-contigs

sort-contigs - Order genome assembly contigs by alignment to reference .fasta

Author: Paul Grablowitz

Source: Github

Description

This python program, sort-contigs, sorts contigs from a query FASTA file based on their alignment to a target reference genome using a PAF (Pairwise Alignments Format) file.

It determines the best matching target contig and optimal orientation (forward or reverse complement) for each query contig, then orders the query contigs along each target contig according to their alignment positions. Unaligned contigs are appended at the end.

Query contigs are assigned to target contigs by identifying the target contigs with the largest sum of aligned bases. Assigned query contigs are ordered along a target contig by identifying the location with the longest alignment. The same alignment is used to define optimal orientation of query contigs respective to assigned target contigs.

The sorted contigs are written to an output FASTA file, with an option to rename them sequentially.

The script uses BioPython for FASTA handling and pandas for PAF file processing.

Usage

The program can be used as in following example:

Alignment

The first step consists of aligning the query genome to the target reference. The code below is a minimal example and may be required to be adjusted for certain conditions.

# Align query assembly to target genome
minimap2 \
	-x asm5 \
	target.fasta \
	query.fasta \
	> alignment.paf

Reordering

The following code shows an example, how to perform reordering of query contigs respective to alignment to target reference.

# Perform reordering steps based on supplied alignment
sort-contigs \
	-p alignment.paf \
	-q query.fasta \
	-t target.fasta \
	-o query-reordered.fasta