MOSAIK is a reference-guided assembler comprising of four main modular programs:
MosaikBuild converts various sequence formats into Mosaik.s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.
The MOSAIK suite was written by Michael Strömberg of the Marth lab at Boston College.
How To Use
There are multiple versions of Mosaik available. An easy way of selecting the version is to use modules. To see the modules available, typemodule avail mosaik
To select a module, typemodule load mosaik/[ver]
where [ver] is the version of choice. This will set your $PATH variable.
Prior to running any programs within the MOSAIK suite, make sure to set the temporary file directory to an appropriate place.
For bash users,export MOSAIK_TMP=/scratch
For cshrc/tcsh users,setenv MOSAIK_TMP /scratch
These declarations can be placed in your ~/.bashrc or ~/.cshrc files instead of at the start of every session.