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ConsensusFixer 0.4

CONTENT:

This java command line application computes a consensus sequence with in-frame insertions and ambiguous nucleotide (wobbles) from ultra deep next-generation sequencing alignments. Provides a list of deletions.

CITATION:

If you use ConsensusFixer, please cite Töpfer A. https://github.com/cbg-ethz/consensusfixer

DOWNLOAD:

Please get the latest binary at releases.

FEATURES:

Calls consensus sequence with a minimal coverage -mcc INT
Integrates consensus sequence into given reference -r ref.fasta
Optionally insert dashes ‘-‘ instead of bases from the reference.
Include insertions with a minimal coverage of -mic INT
Optionally, only include in-frame insertions -f
Calls amibiguous bases (wobbles) if relative base abundance is above -plurality DOUBLE
Performs majority vote, respecting pluralityN, -m
Calls N if relative gap abundance is above -pluralityN DOUBLE
Remove gaps if they are >= pluralityN, -d
Add only the major insertion, -mi
Add all insertions with a distance of at least n bp -pi and -pis INT
Low memory footprint, but only single core, -s
Position-wise statistics about the alignment and a list of deletions, --stats

ISSUES:

Please open an issue on github

PREREQUISITES TO RUN:

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

RUN:

java -jar ConsensusFixer.jar -i alignment.bam -r reference.fasta

  -i          INPUT  : Alignment file in BAM format (required).
  -r          INPUT  : Reference file in FASTA format (optional).
  -o          PATH   : Path to the output directory (default: current directory).
  -mcc        INT    : Minimal coverage to call consensus.
  -mic        INT    : Minimal coverage to call insertion.
  -plurality  DOUBLE : Minimal relative position-wise base occurence to integrate into wobble (default: 0.05).
  -pluralityN DOUBLE : Minimal relative position-wise gap occurence call N (default: 0.5).
  -mi                : Only the insertion with the maximum frequency greater than mic is incorporated.
  -pi                : Progressive insertion mode, respecting mic.
  -pis        INT    : Window size for progressive insertion mode (default: 300).
  -m                 : Majority vote respecting pluralityN first, otherwise allow wobbles.
  -f                 : Only allow in frame insertions.
  -d                 : Remove gaps if they are >= pluralityN.
  -dash              : Use '-' instead of bases from the reference.
  -s                 : Single core mode with low memory footprint.

Technical details

To minimize the memory consumption and the number of full garbage collector executions, use:

java -XX:NewRatio=9 -jar ConsensusFixer.jar

If your dataset is very large and you run out of memory, increase the heapspace with:

java -XX:NewRatio=9 -Xms2G -Xmx10G -jar ConsensusFixer.jar

On multicore systems:

java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar ConsensusFixer.jar

On multi-CPU systems:

java -XX:+UseParallelGC -XX:+UseNUMA -XX:NewRatio=9 -Xms2G -Xmx10G -jar ConsensusFixer.jar

Help:

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

PREREQUISITES COMPILE (only for dev):

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

INSTALL (only for dev):

cd ConsensusFixer
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 ConsensusFixer/target/ConsensusFixer.jar

CONTACT:

Armin Töpfer
armin.toepfer (at) gmail.com
http://www.armintoepfer.com

Contributors

Armin Töpfer
Nina A.H. Madsen

LICENSE:

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