SeqPig is a library of import and export functions for file formats commonly used in bioinformatics for Apache Pig. Additionally, it provides a collection of Pig user-defined functions (UDF's) that allow for processing of aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output and FASTA input. It is built on top of the Hadoop-BAM library. Fore more information see http://seqpig.sourceforge.net/ and the documentation that comes with the release. Releases of SeqPig come bundled with Picard/Samtools, which were developed at the Wellcome Trust Sanger Institute, and Biodoop/Seal, which were developed at the Center for Advanced Studies, Research and Development in Sardinia. See http://samtools.sourceforge.net/ http://biodoop-seal.sourceforge.net/ Installation with precompiled Seal library > mvn install:install-file -Dfile=lib/seal-0.4.0-with-hadoop-bam-7.4.0.jar -DgroupId=it.crs4 -DartifactId=seal -Dversion=0.4.0-with-hadoop-bam-7.4.0 -Dpackaging=jar -DgeneratePom=true > mvn package -DskipTests
HadoopGenomics/SeqPig
SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data.
Java