ProphAsm – compressing k-mer sets via assembling contigs.
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README.md

ProphAsm

Build Status

Prerequisities

  • GCC 4.8+ or equivalent
  • ZLib

Getting started

git clone https://github.com/prophyle/prophasm
cd prophasm && make -j
./prophasm -k 15 -i tests/test1.fa -i tests/test2.fa -o _out1.fa -o _out2.fa -x _intersect.fa -s _stats.tsv

Command line parameters

Program:  prophasm (a greedy assembler for k-mer set compression)
Version:  0.1.0
Contact:  Karel Brinda <kbrinda@hsph.harvard.edu>

Usage:    prophasm [options]

Examples: prophasm -k 15 -i f1.fa -i f2.fa -x fx.fa
             - compute intersection of f1 and f2
          prophasm -k 15 -i f1.fa -i f2.fa -x fx.fa -o g1.fa -o g2.fa
             - compute intersection of f1 and f2, and subtract it from them
          prophasm -k 15 -i f1.fa -o g1.fa
             - re-assemble f1 to g1

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.
 -S       Silent mode.

Note that '-' can be used for standard input/output.

Algorithm

Greedy assemblySubtraction of k-mer sets

Issues

Please use Github issues.

Changelog

See Releases.

Licence

MIT

Author

Karel Brinda <kbrinda@hsph.harvard.edu>