Name: ADEPT
Owner: Los Alamos National Laboratory
Description: ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution for the dataset being analyzed.
Created: 2015-07-24 19:27:31.0
Updated: 2015-07-24 19:27:35.0
Pushed: 2015-08-03 15:59:44.0
Homepage: null
Size: 20328
Language: Perl
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ADEPT, a dynamic next generation sequencing data error-detection program with trimming
======= ADEPT is a program that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution for the dataset being analyzed.
Trimming by quality 5 and filtering reads with any ambiguous base or low complexity.
$ perl ADEPT.pl -p 'reads1.fastq reads2.fastq' -d out_directory
perl ADEPT.pl [options] [-u unpaired.fastq] -p 'reads1.fastq reads2.fastq' -d out_directory
Input File: (can use more than once fastq file)
-u Unpaired reads
-p Paired reads in two files and separate by space in quote
Trim:
-qE 5" and 3" ends triming # as quality level (0-40) (default 5) for trimming
-qC threhold to call a base to be correct (0-1.0) (default = 0.25, higher quality
than 25% the nucleotides at that position within the sampled run )
-qW threhold to identifying a nucleotide as an error if it falls below a defined
percentage of the quality scores for that position (0-1.0) (default = 0)
-qMN ratio of the of the base quality to the qualities of upstream and downstream positions (0-1.0)
By default, all qIN ratios must be at least 0.4 to be considered as a potential erroneous base
(i.e. all adjacent qualities must be at least 2.5 times higher than the quality of the position being investigated).
-qNS threhold to identify a nucleotide as an potential error if its neighbors' quality falls below a defined
percentage of the quality scores for that neighbors' position within the sampled run (0-1.0) (default = 0.3)
Filters:
-min_L Trimmed sequence length will have at least minimum length (default:50)
Q_Format:
-ascii Encoding type: 33 or 64 or autoCheck (default)
Type of ASCII encoding: 33 (standard) or 64 (illumina 1.3+)
-out_ascii Output encoding. (default: 33)
Output:
-prefix Output file prefix. (default: QC)
-stats Statistical numbers output file (default: prefix.stats.txt)
-d Output directory.
Options:
-t # of CPUs to run the script (default:2 )
-split_size Split the input file into several sub files by sequence number (default: 1000000)
-out_non_trim_reads <bool> Output not trimmed reads to prefix.discard.fastq (default: 0, not output)
-debug keep intermediate files
======== Version 1.1 Stable function release. Features:
Los Alamos National Security, LLC (LANS) owns the copyright to ADEPT, which it identifies internally as LA-CC-14-081. The license is GPLv3. See LICENSE for the full text.