ReferenceIndexer

The following auxiliary files for the reference fasta sequence will be created:

1. An index file (.fai) using the 'samtools faidx' command.
2. Sequence dictionary file (.dict) using Picard 'CreateSequenceDictionary'
3. Aligner index files using the specified aligner's index builder. The index produced depends on the chosen aligner and various options. The aligner, genome file and genome length (bwa) should be specified using parameters. Colorspace indexing must be enabled for colorspace data. Additional software specific options can be added using the parameter 'options'. If no aligner is chosen ('none' value) this step will be skipped.

Complete documentation:

Version	1.0
Bundle	sequencing
Categories	Alignment
Authors	Rony Lindell (rony.lindell@helsinki.fi)
Issue tracker	View/Report issues
Source files	component.xml function.scala
Usage	Example with default values ReferenceIndexer( reference = FASTA, aligner = <string>, colorspace = false, length = "long", options = "", picard = "/opt/share/picard/" )

Inputs

Name	Type	Mandatory	Description
reference	FASTA	Mandatory	Reference fasta file to index.

Name	Type	Description
index	FASTA	The reference fasta file along with the created index files.

Name	Type	Default	Description
aligner	string	(no default)	The aligner for which to produce the reference index files. If 'none' is chosen, only the fasta index .fai file and sequence dictionary .dict file will be created. For Tophat alignment choose the Bowtie version you are about to use. Values: {none, bwa, bowtie, bowtie2}
colorspace	boolean	false	For alignment of colorspace sequences colorspace specific indexes must be used. This is not supported in Bowtie2 alignment.
length	string	"long"	Different algorithm may be used by aligners depending on genome length. Human size genomes are long, while bacterial size genomes are short. Values: {long, short}
options	string	""	This string will be added to the command and can include any number of options in the software specific format.
picard	string	"/opt/share/picard/"	Path to Picard directory, e.g. "/opt/picard", which containg the Picard-tools .jar files. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the Picard directory.

Test case	Parameters▼	IN reference	OUT index
case1_bwa	properties	reference	(missing)
	# Create bwa index files, picard=, aligner=bwa, length=short
case2_bowtie	properties	reference	(missing)
	# Create bwa index files, picard=, aligner=bowtie, colorspace=true, options=--seed 8
case3_none	properties	reference	(missing)
	# Create bwa index files, picard=, aligner=none
case4_bowtie2	properties	reference	(missing)
	# Create bwa index files, picard=, aligner=bowtie2

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