Difference between revisions of "SeqMap"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| Line 34: | Line 34: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:24, 6 December 2019
Description
SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC.
Required Modules
Serial
- seqmap
System Variables
- HPC_SEQMAP_DIR - installation directory
- HPC_SEQMAP_BIN - executable directory
- HPC_SEQMAP_DOC - documentation directory
Citation
If you publish research that uses seqmap you have to cite it as follows:
Jiang, H., Wong, W.H. (2008) SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome, Bioinformatics, 24(20)
Validation
- Validated 4/5/2018