CRAM toolkit 3.0 – Read and Write CRAM/BAM Files

CRAM toolkit 3.0

:: DESCRIPTION

The CRAM toolkit is a Java program for writing and reading CRAM files. The CRAM format, based on the research paper Efficient storage of high throughput DNA sequencing data using reference-based compression, will be described in detail in a separate specification. Briefly, the CRAM format is based on efficient compression of DNA sequences by storing only differences between aligned and reference sequences with provision for reads that do not map to the reference. The CRAM format is expected to dramatically lower the storage cost for archiving re-sequencing reads.

::DEVELOPER

The European Nucleotide Archive

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  CRAM toolkit

:: MORE INFORMATION

Citation:

Genome Res. 2011 May;21(5):734-40. Epub 2011 Jan 18.
Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.

Alview 20150902 – Alignment View for BAM files

Alview 20150902

:: DESCRIPTION

Alview (Alignment Viewer) is a fast,portable tool for viewing short reads as native GUI program

:: DESCRIPTION

National Cancer Informatics Program

:: SCREENSHOTS

Alview

:: REQUIREMENTS

  • Windows/Linux/ MacOsX

:: DOWNLOAD

 Alview

:: MORE INFORMATION

Citation

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.
Finney RP, Chen QR, Nguyen CV, Hsu CH, Yan C, Hu Y, Abawi M, Bian X, Meerzaman DM.
Cancer Inform. 2015 Sep 13;14:105-7. doi: 10.4137/CIN.S26470.

Quip 1.1.8 – Aggressive Compression of FASTQ and SAM/BAM files

Quip 1.1.8

:: DESCRIPTION

Quip compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.

::DEVELOPER

Daniel C. Jones

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Quip

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Dec;40(22):e171. doi: 10.1093/nar/gks754. Epub 2012 Aug 16.
Compression of next-generation sequencing reads aided by highly efficient de novo assembly.
Jones DC, Ruzzo WL, Peng X, Katze MG.

Samscope 1.6.6.91 – Lightweight SAM/BAM File Viewer

Samscope 1.6.6.91

:: DESCRIPTION

Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun!Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ features like polarity. The paging-friendly binary file layout makes it feasible to browse data sets far larger than the system’s available RAM.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

Samscope

:: REQUIREMENTS

  • Linux 

:: DOWNLOAD

 Samscope

:: MORE INFORMATION

Citation

Bioinformatics. 2012 May 1;28(9):1276-7. doi: 10.1093/bioinformatics/bts122. Epub 2012 Mar 13.
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
Popendorf K, Sakakibara Y.