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#MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

##Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved contig set based on OLC based assembly. All overlap parameters (Minimum Overlap Length, Identity, etc) are user-declarable at runtime. It is written to run on Linux.

##Requirements: You will need to have the following tools installed and in $PATH, or added to $binpath in the tool:

• Newbler (specifically runAssembly)
• Minimus2 (part of AMOS, also requires MUMmer)

###Installation notes: MUMmer: For larger genome projects, the MUMmer package must be compiled in 64 bit mode. This can be accomplished using: make all CPPFLAGS="-O3 -DSIXTYFOURBITS"

AMOS: For installation of AMOS, AMOS tools must be able to find nucmer, delta-filter and show-coords as compiled above, either by adding it to the path before running ./configure Or by specifying variables: NUCMER,DELTAFILTER, and SHOWCOORDS when running ./configure in the amos directory. Example: ./configure NUCMER=/usr/local/bin/nucmer/bin/nucmer --prefix /usr/local/amos

##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 Turns on debug information

-force Force overwrite of previous runs.

-single_genome=1 Runs assuming single genome, reducing auto-options (one newbler run, exclude fewer contigs, overrides -minLen and minIncludeLen)

##Citation Please cite:

Scholz, M., Lo, C.-C., & Chain, P. S. G. (2014). Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs. Scientific Reports, 4, 6480. Retrieved from http://dx.doi.org/10.1038/srep06480

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