Galaxy |

Racon (version 1.5.0+galaxy1)

Sequences:

input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction

Overlaps:

input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences

Target sequences:

Input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected

Include unpolished:

Output unpolished target sequences

Fragment correction:

Perform fragment correction instead of contig polishing. Note: overlaps file should contain dual/self overlaps

Window length:

Size of window on which POA is performed

Quality threshold:

Threshold for average base quality of windows used in POA

Error threshold:

Maximum allowed error rate used for filtering overlaps

No trimming:

Disables consensus trimming at window ends

Match score:

Score for matching bases. Defalt: 3

Mismatch score:

Score for mismatching bases. Default: -5

Gap penalty:

What it does

Consensus module for raw de novo DNA assembly of long uncorrected reads.

Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.

Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected.

Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in SAM format. Output is a set of polished contigs in FASTA format printed to stdout.

Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs to contain pairwise overlaps between reads including dual overlaps.