Introduction

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/BamHashpmelsted@hi.is.

Publications

  1. BamHash: a checksum program for verifying the integrity of sequence data.
    Cite this
    Óskarsdóttir A, Másson G, Melsted P, 2016-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Arna Óskarsdóttir
    Developer

    deCODE Genetics/Amgen, Reykjavík, Iceland

  2. Gísli Másson
    Developer

    deCODE Genetics/Amgen, Reykjavík, Iceland

  3. Páll Melsted
    Investigator

    deCODE Genetics/Amgen, Reykjavík, Iceland

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Summary
AccessionBT001702
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionIceland
Submitted ByPáll Melsted