pear

pair-end

read

merge

Description

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

Type

bash_script

License

CC-BY-NC-SA-3.0

Keywords

pair-end

read

merge

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
assembled: "$id.$key.assembled"  
unassembled_forward: "$id.$key.unassembled_forward"  
unassembled_reverse: "$id.$key.unassembled_reverse"  
discarded: "$id.$key.discarded"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/pear/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--forward_fastq -f	file required	Forward paired-end FASTQ file
--reverse_fastq -r	file required	Reverse paired-end FASTQ file

Name

Type & Properties

--forward_fastq

-f

file

required

--reverse_fastq

-r

file

required

Outputs

Name	Type & Properties	Description
--assembled	file required output	The output file containing assembled reads. Can be compressed with gzip.
--unassembled_forward	file required output	The output file containing forward reads that could not be assembled. Can be compressed with gzip.
--unassembled_reverse	file required output	The output file containing reverse reads that could not be assembled. Can be compressed with gzip.
--discarded	file required output	The output file containing reads that were discarded due to too low quality or too many uncalled bases. Can be compressed with gzip.

Name

Type & Properties

--assembled

file

required

output

--unassembled_forward

file

required

output

--unassembled_reverse

file

required

output

--discarded

file

required

output

Arguments

Name	Type & Properties	Description
--p_value -p	double	Specify a p-value for the statistical test. If the computed p-value of a possible assembly exceeds the specified p-value then paired-end read will not be assembled. Valid options are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables the test.
--min_overlap -v	integer	Specify the minimum overlap size. The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles.
--max_assembly_length -m	integer	Specify the maximum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long.
--min_assembly_length -n	integer	Specify the minimum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short.
--min_trim_length -t	integer	Specify the minimum length of reads after trimming the low quality part (see option -q)
--quality_threshold -q	integer	Specify the quality threshold for trimming the low quality part of a read. If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed.
--max_uncalled_base -u	double	Specify the maximal proportion of uncalled bases in a read. Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases.
--test_method -g	integer	Specify the type of statistical test. Two options are available. 1: Given the minimum allowed overlap, test using the highest OES. Note that due to its discrete nature, this test usually yields a lower p-value for the assembled read than the cut- off (specified by -p). For example, setting the cut-off to 0.05 using this test, the assembled reads might have an actual p-value of 0.02. 2. Use the acceptance probability (m.a.p). This test methods computes the same probability as test method 1. However, it assumes that the minimal overlap is the observed overlap with the highest OES, instead of the one specified by -v. Therefore, this is not a valid statistical test and the 'p-value' is in fact the maximal probability for accepting the assembly. Nevertheless, we observed in practice that for the case the actual overlap sizes are relatively small, test 2 can correctly assemble more reads with only slightly higher false-positive rate.
--emperical_freqs -e	boolean_true	Disable empirical base frequencies.
--score_method -s	integer	Specify the scoring method. 1. OES with +1 for match and -1 for mismatch. 2: Assembly score (AS). Use +1 for match and -1 for mismatch multiplied by base quality scores. 3: Ignore quality scores and use +1 for a match and -1 for a mismatch.
--phred_base -b	integer	Base PHRED quality score.
--cap -c	integer	Specify the upper bound for the resulting quality score. If set to zero, capping is disabled.
--nbase -z	boolean_true	When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases

Name

Type & Properties

--p_value

-p

double

--min_overlap

-v

integer

--max_assembly_length

-m

integer

--min_assembly_length

-n

integer

--min_trim_length

-t

integer

--quality_threshold

-q

integer

--max_uncalled_base

-u

double

--test_method

-g

integer

--emperical_freqs

-e

boolean_true

--score_method

-s

integer

--phred_base

-b

integer

--cap

-c

integer

--nbase

-z

boolean_true