MetaCompassv1.0

Last updated: Sept 30th, 2015

REQUIREMENTS:

GNU C/C++; Perl; BLAST; Bowtie 2

INSTALLATION:

git clone https://github.com/marbl/MetaCompass.git
cd MetaCompassv1.0
./install.pl

USAGE

RUN METACOMPASS: -- I have a set of metagenomic reads, and want to perform comparative assembly.

./metacompass.pl -f/-q <input FASTA/FASTQ reads> [options] 

-- I know the reference genomes, or I want to perform comparative assembly for a particular genome.

./metacompass.pl -f/-q [input FASTA/FASTQ reads] -r [reference genomes in FASTA] [options]

-- You can try MetaCompass on two test data sets. For a small data set assuming reference genomes are known:

./metacompass.pl -f test/small.reads.fna -r test/small.refgeno.fna -o test1_out

For a big data set assuming reference genomes are known:

./metacompass.pl -f test/big.reads.fna -r test/big.refgeno.fna -o test2_out

For a big data set assuming reference genomes are NOT known:

./metacompass.pl -f test/big.reads.fna -o test3_out

Output:

  Assembled contigs:
            contigs_[iteration #].fasta
  
  Taxonomic profiling output from MetaPhyler:
            mc.classification; mc.[species|genus|family|order|class|phylum].taxprof
  
  Selected Reference genomes:
            mc.refseq.fasta