BamHash: a checksum program for verifying the integrity of sequence data

Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Because the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure tha...

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Bibliographic Details
Published in:	Bioinformatics 2016-01, Vol.32 (1), p.140-141
Main Authors:	Óskarsdóttir, Arna, Másson, Gísli, Melsted, Páll
Format:	Article
Language:	eng
Subjects:	Alignment Bioinformatics Computer programs Humans Integrity Raw Redundant Reproducibility of Results Sequence Analysis Sequencing Software Statistics as Topic
Online Access:	Get full text
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Summary:	Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Because the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing read after alignment, without the loss of data. The software is implemented in C++, GPL licensed and available at https://github.com/DecodeGenetics/BamHash pmelsted@hi.is.
ISSN:	1367-4803 1367-4811 1460-2059