OpenCGA Alignment Engine provides a solution to storage and process sequence alignment data from Next-Generation Sequencing (NGS) projects. The Alignment Engine supports the most common alignment file formats, i.e.: SAM, BAM and CRAM, and takes the alignment data model specification from GA4GH and the implementation from OpenCB GA4GH. See a full description at Alignment Data Model.

We do not define or endorse any dedicated unaligned sequence data format. Instead we recommend storing such data in one of the alignment formats (SAM, BAM, or CRAM) with the unmapped flag set

In addtion, OpenCGA

provides wrappers to the following third-party alignment software packages:

• FastQC: a quality control tool for high throughput sequence data.
• BWA: a software package for mapping low-divergent sequences against a large reference genome.
• Samtools: a program for interacting with high-throughput sequencing data in SAM, BAM and CRAM formats.
• deepTools: a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

OpenCGA Alignment User Interfaces

OpenCGA provides two interfaces to allow users execute the alignment tools and analysis:

• Command line inteface
• RESTful web services interface

OpenCGA command line interface

The OpenCGA command line interface to manage alignment data is accessible through the script opencga.sh using the command alignments:

$ ./opencga.sh alignments

Usage:   opencga.sh alignments <subcommand> [options]

Subcommands:
         index  Index alignment file
         query  Search over indexed alignments
     stats-run  Compute stats for a given alignment file
    stats-info  Retrieve stats for a given alignment file
   stats-query  Fetch alignment files according to their stats
  coverage-run  Compute coverage for a given alignemnt file
coverage-query  Query the coverage of an alignment file for regions or genes
coverage-ratio  Compute coverage ratio from file #1 vs file #2, (e.g. somatic vs germline)
           bwa  BWA is a software package for mapping low-divergent sequences against a large reference genome.
      samtools  Samtools is a program for interacting with high-throughput sequencing data in SAM, BAM and CRAM formats.
     deeptools  Deeptools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
        fastqc  A quality control tool for high throughput sequence data.

The tutorial Working with Alignment Data shows how to use the OpenCGA alignment commandline.

OpenCGA RESTful web services interface

Next image shows the OpenCGA RESTfull web services to manage alignment data: