What it does

SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.

Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus.

Currently this tool works well with and has been tested on 30x diploid coverage genome sequencing data from Illumina and ABI SOLiD technology. This tool may not work well with 454 data, as indels are a significant error mode for 454 data.

Please cite the website "http://srma.sourceforge.net" as well as:

Homer N, and Nelson SF. SRMA: short read micro re-aligner. 2010.

Know what you are doing

There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to understand the parameters by carefully reading the documentation and experimenting. Fortunately, Galaxy makes experimenting easy.

Input formats

SRMA accepts a BAM input file. Note that this file should have been generated from a SAM file which contains the header.

Outputs

The output is in BAM format, see http://samtools.sourceforge.net for more details.

SRMA settings

All of the options have a default value. You can change any of them. Most of the options in SRMA have been implemented here.

SRMA parameter list

This is an exhaustive list of SRMA options:

For SRMA:

INPUT=File
I=File                        The input SAM or BAM file. Required.

OUTPUT=File
O=File                        The output SAM or BAM file. Default value: null.

REFERENCE=File
R=File                        The reference FASTA file. Required.

OFFSET=Integer                The alignment offset. Default value: 20. This option can be set to 'null' to clear the
                              default value.

MIN_MAPQ=Integer              The minimum mapping quality. Default value: 0. This option can be set to 'null' to clear
                              the default value.

MINIMUM_ALLELE_PROBABILITY=Double
                              The minimum allele probability conditioned on coverage (for the binomial quantile).
                              Default value: 0.1. This option can be set to 'null' to clear the default value.

MINIMUM_ALLELE_COVERAGE=Integer
                              The minimum haploid coverage for the consensus. Default value: 3. This option can be set
                              to 'null' to clear the default value.

RANGE=String                  A range to examine. Default value: null.

CORRECT_BASES=Boolean         Correct bases. Default value: false. This option can be set to 'null' to clear the
                              default value. Possible values: {true, false}

USE_SEQUENCE_QUALITIES=BooleanUse sequence qualities Default value: true. This option can be set to 'null' to clear the
                              default value. Possible values: {true, false}

MAX_HEAP_SIZE=Integer         The maximum number of nodes on the heap before re-alignment is ignored Default value:
                              8192. This option can be set to 'null' to clear the default value.