Racon

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Description

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 MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip (which will have impact on parsing time).

License

The MIT License

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of racon and load default version of racon as

module avail racon/ # list available modules
module load racon   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail racon

and choose explicit version you want to use.

Documentation

https://github.com/isovic/racon

Homepage

https://github.com/isovic/racon