Name: MeGAMerge
Owner: Los Alamos National Laboratory
Description: MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
Created: 2015-07-24 19:27:39.0
Updated: 2015-07-24 19:27:40.0
Pushed: 2015-08-03 16:41:43.0
Homepage: null
Size: 112
Language: Perl
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MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
MeGAMerge is a perl tool to accept any number of files containing assembled contigs of any length in Multi-FASTA format, and produce an improved assembly based on OLC based assembly. All overlap parameters (Minimum Overlap Length, Identity, etc) are user-declarable at runtime.
Requirements:
Must have the following tools installed and in PATH, or added to $binpath in the tool:
-Newbler (specifically runAssembly)
-Minimus2 (part of AMOS, requires MUMMer)
Usage:
MeGAMerge-1.0.pl [options] output_directory
Options:
-overlap=NN Parameter for minimum overlap length in minimus2/Newbler (default = 80)
-minID=NN Minimum % identity for overlap in minimus2/Newlber (default 98)
-conserr=NN Maximum conservation error for minimus2 (default 0.06)
-cpu=NN Number of CPU for Newbler (default 4)
-bindir=directory Directory containing MUMmer executables and AMOS executables
-newblerdir=direcoty Directory for newbler executable (runAssembly)
-o=outfile Name of final file to output in output_directory (default MergedContigs.fasta)
-minLen=NN Minimum length to include in newbler assemblies (default 150)
-minIncludeLen=NN Minimum length to include in minimus assembly (default, 200)
-d=1 Turns on debug information
-single_genome=1 Runs assuming single genome, reducing auto-options
(one newbler run, exclude fewer contigs, overrides -minLen and minIncludeLen)
Los Alamos National Security, LLC (LANS) owns the copyright to MeGAMerge, which it identifies internally as CODE-2012-145. The license is GPLv3. See LICENSE for the full text.