MetaCompass V1.0
Comparative Assembly for Metagenomic Sequences
Author: boliu@umiacs.umd.edu
Date: Sun Sep  9 22:02:11 EDT 2012



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



INSTALLATION:
./install.pl



RUN METACOMPASS:
-- I have a set of metagenomic reads, and want to perform comparative assembly.
./metacompass.pl [input FASTA reads] [output prefix] [directory of Bowtie 2] [# iterations] [# threads]


-- I know the reference genomes, or I want to perform comparative assembly for a particular genome.
./bin/compass.pl [input FASTA reads] [reference genome] [output prefix] [directory of Bowtie 2] [# iterations] [# threads]


-- You can try MetaCompass on two test data sets.
For a small data set assuming reference genomes are known:
./bin/compass.pl ./test/small.reads.fna ./test/small.refgeno.fna ./test/small [directory of Bowtie 2] 1 1

For a big data set assuming reference genomes are known:
./bin/compass.pl ./test/big.reads.fna ./test/big.refgeno.fna ./test/big [directory of Bowtie 2] 1 1

For a big data set assuming reference genomes are NOT known:
./metacompass.pl ./test/big.reads.fna ./test/big [directory of Bowtie 2] 1 1



QUESTIONS:
Contact Bo Liu at boliu@umiacs.umd.edu