Up: Component summary Function

ReferenceIndexer

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

Complete documentation:

CreateSequenceDictionary (picard-tools)

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

Inputs

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

Outputs

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

Parameters

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 cases

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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