8000 GitHub - armintoepfer/profilesim: Creating profiles for SimSeq from BAM alignments and a set of reference genomes.
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ProfileSim

Creates a profile file for SimSeq, given a BAM alignment and a set of references in FASTA format. Only conserved regions across the references are taken into consideration.


PREREQUISITES TO RUN:

RUN:

java -jar ProfileSim.jar -i alignment.bam -g references.fasta

Restrict to a certain area of the genome

java -jar ProfileSim.jar -i alignment.bam -g references.fasta -r 300-4590

Technical details

#####To minimize the memory consumption and the number of full garbage collector executions, use: java -XX:NewRatio=9 -jar ProfileSim.jar

#####If your dataset is very large and you run out of memory, increase the heapspace with: java -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar

####On multicore systems: java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar

####On multi-CPU systems: java -XX:+UseParallelGC -XX:+UseNUMA -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar

#####Unix wrapper: function psim() { java -XX:+UseParallelGC -Xms2g -Xmx10g -XX:+UseNUMA -XX:NewRatio=9 -jar ~/ProfileSim.jar $*; }

Help:

Help can be shown by running without additional parameters: java -jar ProfileSim.jar

PREREQUISITES COMPILE (only for dev):

INSTALL (only for dev):

cd ProfileSim
mvn -DartifactId=samtools -DgroupId=net.sf -Dversion=1.8.9 -Dpackaging=jar -Dfile=src/main/resources/jars/sam-1.89.jar -DgeneratePom=false install:install-file
mvn clean package
java -jar ProfileSim/target/ProfileSim.jar

CONTACT:

Armin Töpfer
armin.toepfer (at) gmail.com
http://www.bsse.ethz.ch/cbg/people/toepfera

LICENSE:

GNU GPLv3 http://www.gnu.org/licenses/gpl-3.0

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Creating profiles for SimSeq from BAM alignments and a set of reference genomes.

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