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

Arna Óskarsdóttir | Zendy; Gísli Másson | Zendy; Páll Melsted | Zendy

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

Author(s) -

Arna Óskarsdóttir,

Gísli Másson,

Páll Melsted

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv539

Subject(s) - checksum , computer science , raw data , software , sequence (biology) , data mining , database , programming language , operating system , biology , genetics

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.

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