ProphAsm2

• Introduction
• Prerequisities
• Getting started
• How to use
• Issues
• Changelog
• Licence
• Contact

Introduction

ProphAsm2 is a versatile tool for computing simplitigs/SPSS from k-mer sets and for k-mer set operations. The new features compared to the original ProphAsm include a largely speed and memory optimization, parallelization, support for k-mer sizes up to 64 and support for minimum abundances.

Various types of sequencing datasets can be used as the input for ProphAsm, including genomes, pan-genomes, metagenomes or sequencing reads. Besides computing simplitigs, ProphAsm can also compute intersection and set differences of k-mer sets (while set unions are easy to compute simply by merging the source files).

Upon execution, ProphAsm first loads all specified datasets (see the -i param) and the corresponding k-mer sets (see the -k param). If the -x param is provided, ProphAsm then computes their intersection, subtracts the intersection from the individual k-mer sets and computes simplitigs for the intersection. If output files are specified (see the -o param), it computes also set differences.

Prerequisites

• GCC 4.8+ or equivalent
• ZLib

Getting started

Download and compile ProphAsm:

git clone https://github.com/prophyle/prophasm2
cd prophasm2 && make -j

Compute simplitigs:

./prophasm -k 31 -i tests/test1.fa -o simplitigs.fa

How to use

Set operations:

./prophasm -k 31 -i tests/test1.fa -i tests/test2.fa -o _out1.fa -o _out2.fa -x _intersect.fa -s _stats.tsv

Command-line arguments

Algorithm

In its core, ProphAsm2 uses the original algorithm for rapid computation of simplitigs as described in the simplitig paper.

def extend_simplitig_forward (K, simplitig):
	extending = True
	while extending:
		extending = False
		q = simplitig[-k+1:]
		for x in ['A', 'C', 'G', 'T']:
			kmer = q + x
			if kmer in K:
				extending = True
				simplitig = simplitig + x
				K.remove (kmer)
				K.remove (reverse_complement (kmer))
				break
	return K, kmer

def get_maximal_simplitig (K, initial_kmer):
	simplitig = initial_kmer
	K.remove (initial_kmer)
	K.remove (reverse_complement (initial_kmer))
	K, simplitig = extend_simplitig_forward (K, simplitig)
	simplitig = reverse_complement (simplitig)
	K, simplitig = extend_simplitig_forward (K, simplitig)
	return K, simplitig

def compute_simplitigs (kmers):
	K = set()
	for kmer in kmers:
		K.add (kmer)
		K.add (reverse_complement(kmer))
	simplitigs = set()
	while |K|>0:
		initial_kmer = K.random()
		K, simplitig = get_maximal_simplitig (K, initial_kmer)
		simplitigs.add (simplitig)
	return simplitigs

Issues

Please use Github issues.

Changelog

See Releases.

Licence

MIT

Contact

Ondrej Sladky <ondra.sladky@gmail.com>
Karel Brinda <karel.brinda@inria.fr>