Difference between revisions of "Mosaik"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| Line 34: | Line 34: | ||
*{{#var:app}} | *{{#var:app}} | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory. |
* HPC_MOSAIK_BIN - executable file directory. | * HPC_MOSAIK_BIN - executable file directory. | ||
* HPC_MOSAIK_NET - network file directory. | * HPC_MOSAIK_NET - network file directory. | ||
Latest revision as of 21:23, 6 December 2019
Description
MOSAIK is a reference-guided assembler comprising of four main modular programs:
- MosaikBuild
- MosaikAligner
- MosaikSort
- MosaikText
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, MosaikText converts alignments to different text-based formats.
At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or the Illumina ELAND formats.
Required Modules
Serial
- mosaik
System Variables
- HPC_MOSAIK_DIR - installation directory.
- HPC_MOSAIK_BIN - executable file directory.
- HPC_MOSAIK_NET - network file directory.
- MOSAIK_TMP - default temporary file directory. Note that HiPerGator2 nodes are diskless, so MOSAIK_TMP must not be set to /tmp.
How To Run
If you would like to use the provided network files with MosaikAligner use the $HPC_MOSAIK_NET variable for the location of network file directory. E.g.
MosaikAligner -annpe $HPC_MOSAIK_NET/2.1.26.pe.100.0065.ann \ -annse $HPC_MOSAIK_NET/2.1.26.se.100.005.ann -in ...
