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 128 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.
- GCC 4.8+ or equivalent
- ZLib
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
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
Usage: prophasm2 [options]
Command-line parameters:
-k INT K-mer size.
-i FILE Input FASTA file (can be used multiple times).
-o FILE Output FASTA file (if used, must be used as many times as -i).
-x FILE Compute intersection, subtract it, save it.
-s FILE Output file with k-mer statistics.
-t INT Number of threads (default 1).
-m INT Minimum abundance of k-mers to appear in the assembly (default 1).
-S Silent mode.
-u Do not consider k-mer and its reverse complement as equivalent.
Note that '-' can be used for standard input/output.
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 simplitigsPlease use Github issues.
See Releases.
Ondrej Sladky <[email protected]>
Karel Brinda <[email protected]>