Map reads module

This module allow to map reads with a mapper program.

• Internal name: mapreads
• Available: Both local and distributed mode


• Input ports:
  • reads: reads in FASTQ format (format: reads_fastq)
  • mapperindex: mapper index for the genome (automatically generated from genome sequence file)
  • genomedescription: genome description (automatically generated from genome sequence file)


• Output port:
  • output: alignments in FASTQ format (format: mapper_results_sam)


• Optional parameters:

Parameter	Type	Description
mapper	string	The name of the mapper to use (e.g. bowtie, bwa, soap, gsnap)



• Optional parameters:

Parameter	Type	Description	Default value
mapper.version	string	Define the version of the mapper to use	See below in the next table
mapper.flavor	string	Define the flavor of the mapper to use (e.g. standard version or large index version)	See below in the next table
mapper.use.bundled.binares	boolean	Use the mapper bundled binaries in Eouslan to perform the mapping. If the value is false, the mapper will be search in the PATH environnment variable	True
local.threads	integer	Define the number of threads to use in local mode.	0 (use the main.local.threads global property)
max.local.threads	integer	Define the maximum number of threads to use in local mode.	0 (no limit)
hadoop.threads	integer	Define the maximum number of threads to use in hadoop mode.	0 (the number of available processors)
mapper.arguments	string	Mapper additional command line arguments	See below in the next table
hadoop.reducer.task.count	integer	The count of Hadoop reducer tasks to use for this step. This parameter is only used in Hadoop mode	Not set



• Available built-in mappers:

Mapper name	Bundled versions	Default version	Flavors	Default Flavor	Default mapper arguments
Bowtie	0.12.9, 1.1.1	0.12.9	standard, large-index	standard	--best -k 2
Bowtie2	2.0.6, 2.2.4	2.0.6	standard, large-index	standard	-k 2
BWA	0.6.2, 0.7.12, 0.7.15	0.6.2	aln, mem	aln	-l 28
GSNAP	2012-07-20, 2014-12-21, 2017-02-25, 2017-04-24	2012-07-20	gsnap, gmap	gsnap	-N 1
STAR	2.4.0k, 2.5.2b, 2.6.1b, 2.7.2d, 2.7.8a	2.7.2d	standard, large-index	standard	--outSAMunmapped Within
Minimap2	2.5, 2.10, 2.12, 2.17, 2.18, 2.24	2.17	standard	standard



• Removed built-in mappers:
• SOAP 2.x


• Configuration example:

<!-- Map reads step -->
<step id="mymappingstep" skip="false" discardoutput="true">
	<module>mapreads</module>
	<parameters>
		<parameter>
			<name>mapper</name>
			<value>star</value>
		</parameter>
		<parameter>
			<name>mapper.version</name>
			<value>2.4.0k</value>
		</parameter>
		<parameter>
			<name>mapper.flavor</name>
			<value>standard</value>
		</parameter>
		<parameter>
			<name>mapper.arguments</name>
			<value>--outSAMunmapped Within</value>
		</parameter>
	</parameters>
</step>

Note 1: In hadoop mode, Eoulsan use the mapreduce.cluster.temp.dir hadoop setting as location for the mapping temporary files (mapper indexes and FASTQ temporary files). This path must be set in the Hadoop client properties.

Note 2: In hadoop mode, use the requiredMemory attribute of the step tag to define the amount of memory required by the mapper in Hadoop mode. By default the value is 8 GB.

Warning: In hadoop mode, the results of BWA are not exactly the same as in local mode because with BWA the SAM output of splitted FASTQ files are not the same as the full FASTQ files (See this BioStar post for more information).