wham_bam

Simple script to convert all fastq files in a directory into bam files

Brought to you by: rabadger

Last Update: 2016-07-06

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The script takes fastq files from sequence runs (or from bam files converted using bam2fastq) and aligns to a user-selected genome.

Additional options to only convert reads above a certain mapping score, removing duplicates and generating bed files (requires Bedtools set in path).

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Registered

2012-10-26

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Hadoop-BAM
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope. See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net