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This program is a sub-routine of SeqAn-Flexbar (a reimplementation of the original flexbar[1]) and removes adapter sequences from reads.
[1] Dodt, M.; Roehr, J.T.; Ahmed, R.; Dieterich, C. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 2012, 1, 895-905.
Options
Input Ports
- FastA file containing the two adapter sequences. The adapters according to the layout: 5'-adapter1-read-adapter2-3'. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2,opt.]
- Either one (single-end) or two (paired-end) read files. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2]
Output Ports
- Name of the output file. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,raw,raw.bgzf,raw.gz,raw.bz2,Inactive]
Views
- SflexAR Std Output
- The text sent to standard out during the execution of SflexAR.
- SflexAR Error Output
- The text sent to standard error during the execution of SflexAR. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
Workflows
- No workflows found
Links
- No links available
Developers
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