Difference between revisions of "SNAP 2016"
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== Introduction == | |||
SNAP, which stands for ''Scalable Nucleotide Alignment Program'' is a fast and accurate read aligner for high-throughput sequencing data. | |||
This SNAP version is not to be confused with the other version of SNAP, namely the Semi-HMM-based Nucleic Acid Parser which you can find [https://wiki.hpcuser.uni-oldenburg.de/index.php?title=SNAP-HMM_2016 here]. | |||
== Installed Version == | |||
These versions are installed and and currently available on environment ''hpc-env/6.4'': | |||
'''SNAP/1.0beta.23'''-foss-2017b | |||
'''SNAP-HMM/2013-11-29'''-GCCcore-6.4.0 | |||
== Using SNAP == | |||
SNAP is installed at the environment hpc-env/6.4 which is to be loaded at first in order to load the SNAP module: | |||
module load hpc-env/6.4 | |||
module load SNAP | |||
''or'' | |||
module load hpc-env/6.4 | |||
module load SNAP-HMM | |||
Now you can proceed according to the scheme ''snap-aligner <command>'' | |||
== Documentation == | |||
For further information please consult the [http://snap.cs.berkeley.edu/#faq developer's website] where you can find a [http://snap.cs.berkeley.edu/downloads/snap-1.0beta-quickstart.pdf quick start guide] as well as a [http://snap.cs.berkeley.edu/downloads/snap-1.0beta-manual.pdf user manual]. | |||
Please note that the commands displayed there may not be transferable one-to-one. In such cases, replace the 'snap' command with 'snap-aligner'. | |||
Latest revision as of 14:26, 28 June 2019
Introduction
SNAP, which stands for Scalable Nucleotide Alignment Program is a fast and accurate read aligner for high-throughput sequencing data. This SNAP version is not to be confused with the other version of SNAP, namely the Semi-HMM-based Nucleic Acid Parser which you can find here.
Installed Version
These versions are installed and and currently available on environment hpc-env/6.4:
SNAP/1.0beta.23-foss-2017b SNAP-HMM/2013-11-29-GCCcore-6.4.0
Using SNAP
SNAP is installed at the environment hpc-env/6.4 which is to be loaded at first in order to load the SNAP module:
module load hpc-env/6.4 module load SNAP or module load hpc-env/6.4 module load SNAP-HMM
Now you can proceed according to the scheme snap-aligner <command>
Documentation
For further information please consult the developer's website where you can find a quick start guide as well as a user manual. Please note that the commands displayed there may not be transferable one-to-one. In such cases, replace the 'snap' command with 'snap-aligner'.
