SequenceAlignmentFixer

CONTENT:

This java command line application is a toolbox, combining a multitude of alignment statistics and fixes for Next Generation Sequencing (NGS) data. Computes consensus sequence with in-frame deletions and insertions

CITATION:

If you use SequenceAlignmentFixer, please cite Töpfer A. https://github.com/armintoepfer/seqalfixer

DOWNLOAD:

Please get the latest binary at https://github.com/armintoepfer/seqalfixer/releases

FEATURES:

Select only a region for analysis
Coverage plot
SNV entropy landscape plot
Consensus sequence:
Gapped, including major in-frame deletions
In-frame insertions are including, with minmal coverage of -insertions INT
Minimal coverage with -coverage INT

WORKFLOW:

A BWA workflow to realign reads against the consensus sequence, please have a look at HOWTO

PREREQUISITES TO RUN:

JDK 7 (http://jdk7.java.net/)

RUN:

java -jar SequenceAlignmentFixer.jar -i alignment.bam
Reads need to be properly aligned.

Reconstruct specific region with respect to reference genome numbering
-r 790-2292

Consensus
--consensus

Minimal coverage of insertions
-insertions INT [default: do not include insertions]

Minimal coverage
-coverage INT [default: 0]

Plots

Summary statistics can be produced with R: R CMD BATCH support/plots.R

Technical details

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

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

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

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

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

Help:

Further help can be showed by running without additional parameters: java -jar SequenceAlignmentFixer.jar

PREREQUISITES COMPILE (only for dev):

Maven 3 (http://maven.apache.org/)

INSTALL (only for dev):

cd SequenceAlignmentFixer
mvn -DartifactId=samtools -DgroupId=net.sf -Dversion=1.9.6 -Dpackaging=jar -Dfile=src/main/resources/jars/sam-1.96.jar -DgeneratePom=false install:install-file
mvn clean package
java -jar SequenceAlignmentFixer/target/SequenceAlignmentFixer.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