MaSuRCA is now on github

MaSuRCA has new home on github at https://github.com/alekseyzimin/masurca. MaSuRCA combines jellyfish, QuORUM, and other modules into one repository. The individual modules are submodules in the repository. The master branch of the masurca repository tracks the latest working commits. To checkout and compile MaSuRCA do the following:

git clone https://github.com/alekseyzimin/masurca

git submodule init

git submodule update

make

MaSuRCA will compile under build/inst/bin/

To create a distribution, run make install. This will create MaSuRCA-3.2.4.tar.gz distributable tarball.

EDIT: to compile MaSuRCA from development tree, you will need the following dependencies:
swig and yaggo (http://www.swig.org/ and https://github.com/gmarcais/yaggo). Both must be available on the path.

Please post all questions and bug reports under "issues" in github: https://github.com/alekseyzimin/masurca/issues

New MaSuRCA version 3.2.4

I have just finished testing a new release of MaSuRCA version 3.2.4. The major improvement in this version is ability to run the hybrid assembly (Illumina+PacBio/Oxford Nanopore data) on a grid.  At this point only SGE is supported, and I am working on SLURM support which will be implemented shortly. Other improvements include:

1. gzippped fasta/fastq input files of PacBio/Oxford Nanopore reads supported
2. general speed and accuracy improvements
3. minor bugfixes based on user feedback

The new version is designed in such a way to allow mammalian genome assembly on a grid of computers with 128Gb of RAM.

The new release is available here
ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/MaSuRCA-3.2.4.tar.gz

I am now updating the MaSuRCA manual to reflect the new options for grid execution, and I will upload it later today.