Filter reads module

This module allow to filter input reads. Currently, this module can trim polyN read tails, remove reads with a short length and discard reads with bad base quality mean. Eoulsan provides a plugin system for reads filters. To enable a filter, a parameter for this filter must be set. If the filter takes no option, add a parameter with the name of the filter as the key and an empty string for the value.

The filters order that will be applied on the reads is the same order of the filters parameters in the workflow file. So the count of the filtered reads by each filter in the log will be different according to the filter parameters order in the workflow file.

When the parameter type is none, the value of the parameter is not read by the filter and it can be left empty.

Warning: Some filters can modify the output reads (e.g. the trimpolynend filter remove the polyN tails of the reads). So a filter like the quality filter will not produce the same output if declared before or after the trim filter.

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


• Input port:
  • input: reads in FASTQ format (format: reads_fastq)


• Output port:
  • output: reads in FASTQ format (format: reads_fastq)


• Optional parameters:

Parameter	Type	Description	Default value	Modify reads
paircheck	none	Check if the identifiers of the two ends had the same identifier if enabled.	N/A	No
pairedend.accept.paired.end	boolean	Remove all paired-end reads if false.	Not set	No
pairedend.accept.single.end	boolean	Remove all single-end reads if false.	Not set	No
illuminaid	none	Remove all reads that not pass illumina filters if enabled.	N/A	No
quality.threshold	float	The threshold for the mean base quality. Unit in decimal quality score	Not set	No
trimpolynend	none	This filter trim polyN tails of reads if enabled.	N/A	Yes
length.minimal.length.threshold	integer	The minimal threshold for the reads length. Unit in bases.	Not set	No
trim.length.threshold	integer	The threshold for the length of the reads. Unit in bases. This filter trim polyN tails of reads. This filter is deprecated, use instead trimpolyn and length.minimal.length.threshold.	Not set	Yes
readnamestartwith.forbidden.prefixes	string	Remove all reads with id that starts with one of prefixes separated by comma.	Not set	No
readnamestartwith.allowed.prefixes	string	Keep only the reads with id that starts with one of prefixes separated by comma.	Not set	No
readnameregex.forbidden.regex	string	Remove all the reads with id that matches with the regular expression.	Not set	No
readnameregex.allowed.regex	string	Keep only the reads with id that matches with the regular expression.	Not set	No
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	N/A
maxlength.maximum.length.threshold	integer	The maximum threshold for the reads length. Unit in bases.	Not set	No
readsequenceregex.forbidden.regex	string	Remove all the reads with pattern that matches with the regular expression.	Not set	No
readsequenceregex.allowed.regex	string	Keep only the reads with pattern that matches with the regular expression.	Not set	No
slidingwindow.arguments	string	Cutting once the average quality within the window falls below a threshold.	Not set	No
trailing.arguments	string	Remove low quality bases from the end.	Not set	No
leading.arguments	string	Remove low quality bases from the beginning.	Not set	No
headcrop.arguments	string	Remove the specified number of bases from beginning of the read.	Not set	No
crop.arguments	string	Remove bases regardless of quality from the end of the read.	Not set	No
nanoporesequencetype.keep	string	Keep only a type of Nanopore reads. Available values are: template, complement and consensus. For 1D sequencing, use consensus value to keep all the reads.	consensus	No
polyatail.minimal.length	integer	Mininal length of polyA/polyT tail. This filter just add a "tail_type" field in the read headers.	10	Header
polyatail.maximal.error.rate	float	Maximal threshold allowed errors in polyA/polyT tails.	0.1	Header
polyatail.minimal.length.for.error.rate.computation	integer	Minimal length of tail sequence before computing the error rate.	5	Header
reversepolyt	none	This filter reverse complements reads with a "tail_type=polyT" field in read header.	N/A	No
removeinvalidpolya.allowed.tail.type	string	This filter will keep only reads with specified value(s) for the "tail_type" field in the read headers. Reads with this field will be discarted.	polyaA,polyT	No
ggghead	none	This filter will search for GGG head and CCC tail and add additional fields in read header fields.	N/A	Header
requireggghead.allow.mismatch	boolean	This filter will remove any sequence without GGG head. This parameter allow one mismatch in the GGG sequence.	true	No

• Configuration example:

<!-- Filter reads step -->
<step id="myfilterreadsstep" skip="false" discardoutput="true">
	<module>filterreads</module>
	<parameters>
		<parameter>
			<name>illuminaid</name>
			<value></value>
		</parameter>
		<parameter>
			<name>trimpolynend</name>
			<value></value>
		</parameter>
		<parameter>
			<name>length.minimal.length.threshold</name>
			<value>40</value>
		</parameter>
		<parameter>
			<name>quality.threshold</name>
			<value>30</value>
		</parameter>
	</parameters>
</step>