Assembler for PacBio reads.
We'll overlap the PacBio reads using the MinHash sketch method proposed in:
Berlin, Konstantin, et al. "Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing." bioRxiv (2014): 008003.
Once the reads are overlapped, we will assemble the reads into a string graph. String graphs are described in:
Myers, Eugene W. "The fragment assembly string graph." Bioinformatics 21.suppl 2 (2005): ii79-ii85.
We do not assume that reads are "correct"; instead, we will maintain "probabilistic" overlaps between the fragments in the string graph. Once we have obtained these probabilistic overlaps, we can estimate the ploidy of each overlap by normalizing the overlap coverage by length and can then apply traditional genotyping methods (e.g., the likelihood estimation stages used in SAMTools) to find the concensus sequences at each overlap.
PacMin uses Maven to build. To build PacMin, cd into the repository and run "mvn package".
ADAM is packaged via appassembler and includes all necessary dependencies
You might want to add the following to your .bashrc to make running adam easier:
alias pacmin=". $PACMIN_HOME/pacmin-cli/target/appassembler/bin/pacmin"
$PACMIN_HOME should be the path to where you have checked PacMin out on your local filesystem.
To change any Java options (e.g., the memory settings --> "-Xmx4g", or to pass Java properties)
set the $JAVA_OPTS environment variable. Additional details about customizing the appassembler
runtime can be found here.
Once this alias is in place, you can run adam by simply typing pacmin at the commandline.
PacMin is released under an Apache 2.0 license.
Snapshots of PacMin are available from the Sonatype OSS repository:
<groupId>org.bdgenomics.pacmin</groupId>
<artifactId>pacmin-core</artifactId>
<version>0.0.1-SNAPSHOT</version>
Once we've got a release, we will publish to Maven Central.