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pRESTO MaskPrimers (version 0.6.2+galaxy0)

Input FASTQ file:

Primer FASTA file:

Mode:

Specifies how identified primer sequences will be handled.

Command:

Max Length:

Maximum length of sequence window to search for primers.

Skip Reverse Complement:

Skip checking of reverse complement sequences.

Gap Open Penalty:

Positive value of the gap open penalty.

Gap Extension Penalty:

Positive value of the gap extension penalty.

Reverse Match:

Match the reverse complement of primer sequences against the ends of reads.

Extract Barcodes (UMIs):

Capture the sequence preceding the primer as a UMI.

Max Error Rate:

Maximum allowable rate between read and primer sequence.

Generate Detailed Log:

Generate detailed log information that can be summarized with ParseLog.

Removes primers and annotates sequences with primer and barcode identifiers

See the pRESTO online help for more information.

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Note about limitations of pRESTO tools within Galaxy:

pRESTO tools in galaxy have the following limitations vs. when run at the command line:

Inputs must be FASTQ format and cannot be FASTA format.
Multiple inputs files are not supported per argument (e.g. -1, -2 or -s), i.e.
- Steps that take a pair of fastq inputs can only take two files, not two sets of files
- Steps that take a single set of fastq inputs can only take a single file
The --outdir and --outname options are not supported; output files are named directly