Alignment and Coverage
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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.: , and takes the alignment data model specification from and the implementation from . See a full description at .
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.
OpenCGA alignment engine provides the following analysis:
Index analysis To index a coordinate-sorted alignment file (BAM or CRAM) for fast random access. This index is needed when region parameters are used to limit the query analysis to particular regions of interest.
Query analysis This analysis outputs those alignments matching the specified filters, such as minimum mapping quality, maximum insert size, maximum number of mismatches in the alignment, properly paired alignments,... In addition, users may specify one or more comma-separated regions to restrict output to only those alignments which overlap the specified region(s). Note that use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
Coverage analysis This analysis takes a coordinate-sorted and indexed alignment file (in BAM or CRAM format) as input and generates a coverage file (in BigWig format). The coverage is calculated as the number of reads per window of a user-defined size, if window size is equal to 1, the coverage is the number of reads per position. Once coverage is computed, the read coverage over multiple genomic regions can be fetched quite quickly.
Statistics analysis OpenCGA computes statistics for a given alignment file by using the . Alignment statistics are indexed in order to allow users to query for alignment files according to those statistics.
In addtion, OpenCGA provides wrappers to the following third-party alignment software packages:
: a quality control tool for high throughput sequence data.
: a software package for mapping low-divergent sequences against a large reference genome.
: a program for interacting with high-throughput sequencing data in SAM, BAM and CRAM formats.
: 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 provides two interfaces to allow users execute the alignment tools and analysis:
Command line inteface
RESTful web services interface
The OpenCGA command line interface to manage alignment data is accessible through the script opencga.sh using the command alignments:
Next image shows the OpenCGA RESTfull web services to manage alignment data:
The tutorial shows how to use the OpenCGA alignment commandline.
