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MaSuRCA - whole genome assembler

Introduction

MaSuRCA (Maryland Super-Read Celera Assembler) is a whole-genome assembly package that can combine short and long reads from different sequencing hardware.  Underlying software includes Jellyfish (k-mer counter), a modified version of the Celera assembler, SuperReads (method for extending short reads) and QuorUM (error corrector for Illumina data).

(Note that a more recent version of the Celera assembler that that packaged with MaSuRCA is available on several WestGrid systems.  See the Celera Whole-Genome Shotgun Assembler page.)

Running MaSuRCA on Breezy

MaSuRCA requires a newer version of Perl than the default on Breezy.

To set up your environment (bash shell example) prior to running MaSuRCA, use:

export PATH=/global/software/perl/perl-5.17.4/bin:$PATH
module load python/2.7.2

The MaSuRCA binaries have been installed in /global/software/masurca/masurca210/bin .


Updated 2013-12-06.

 

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