Commit 5efdb254 authored by Jerome Mariette's avatar Jerome Mariette
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add 16Scleaner documentation

parent e740dc6c
The 16Scleaner will enable you to trim off primer sequences, cull sequences based on sequence length, the presence of ambiguous bases and the
presence of homopolymers and get the reverse complement of your sequences.
<li>input file: This program accepts sff/fasta/fastq files as input.</li>
<li>qual file list: If a fasta file is used as input a qual file can be provided (has to be named input_file.qual or input_file.fasta.qual).</li>
<li>ng6cfg file: The NG6 run config file the analyse belongs to.</li>
<li>project id: The NG6 project id the analyse belongs to.</li>
Outputs a cleaned file in the same format as the input (fasta if sff is provided) and a log file.
<li>cleaning options, choose one or more between:
<li>--clean-length, Filter reads with a legnth in between [x:y]</li>
<li>--clean-ns, Filter reads with to many N</li>
<li>--clean-homopolymers, Filter reads with homopolymers higher than the homopolymer_length parameters</li>
<li>--switch-strand, Orients the reads considering the strand</li>
<li>--trim, Trim the sequence when primers are found</li>
<li>--clean-full-length, Clean reads if fwd and rvrs primer found and if length shorter than full_length_min_size parameters</li>
<li>fwd primer: The forward primer sequence,</li>
<li>fwd minmatch: The min number of matches allowed for the forward primer,</li>
<li>rvrs primer: The reverse primer sequence,</li>
<li>rvrs minmatch: The min number of matches allowed for the reverse primer,</li>
<li>min length: Minimal length,</li>
<li>max length: Maximal length,</li>
<li>ns percent: Percentage of N to use to filter reads,</li>
<li>homopolyler length: Max homopolymer size,</li>
<li>min full length length: Min full length sequences size,</li>
<li>analyse name: The analyse name to display in ng6,</li>
<li>analyse description: The analyse description to display in ng6,</li>
<li>results archive name: The results archive name to display in ng6.</li>
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