RECKONER - Read Error Corrector Based on KMC

RECKONER

RECKONER is a tool for correction of Illumina reads. It is based on the error correction algorithm BLESS and utilizes the following tools:

• KMC3 for k-mer counting,
• KMC tools for trimming a k-mer database.

RECKONER is available for Linux and Windows.

Compilation

To compile RECKONER in Linux use g++ version 4.9.2 or newer by typing "make" in the project directory, as a result there will be generated executable files in the "bin" directory.

To compile RECKONER in Windows open file "RECKONER.sln" in Visual Studio 2015, select "Release" from the drop-down list. Then click "Build" and "Build Solution" from the main menu.

Running

To run RECKONER in Linux execute file "reckoner" from the "bin" directory (typically by typing "./reckoner ARGUMENTS").

To run RECKONER in Windows execute file "reckoner.exe" from the "bin" directory (typically by typing "reckoner.exe ARGUMENTS" from the command line).

As ARGUMENTS type the following:

• -help - prints short help,
• -read FASTQ_FILE - input FASTQ read file name (possibly gzipped), can be passed many times,
• -prefix DIRECTORY - directory for temporary and output files, (optional, default current directory (.)),
• -kmerlength K - length of k-mers (optional),
• -genome G - approximate genome size (optional),
• -memory N - max k-mer counting memory consumption in GB (optional, default 4),
• -extend N - max extend length, (optional, default 2),
• -threads N - number of correcting threads, (optional, default number of available virtual cores).

If k-mer length is not given it is determined automatically. Passing the approximate genome size may slightly improve k-mer length calculation.

Instead of using -read option the input FASTQ files can be specified at the end of the command line.

To correct paired-end files simply pass both of them as two single-end files.

Result files will be created in the output directory with a "corrected" suffix.

Examples:

./reckoner -kmerlength 25 -prefix results -threads 16 -read SRR088579.fastq.gz
./reckoner -read ERR729973.fastq -read ERR729974.fastq
./reckoner -kmerlength 30 ERR729973.fastq ERR729974.fastq
./reckoner -kmerlength 20 ERR422544_1.fastq.gz ERR422544_2.fastq.gz

Miscellaneous

• Homepage: http://sun.aei.polsl.pl/REFRESH/
• Contact: maciej.dlugosz@polsl.pl
• RECKONER is distributed under license GPL 3.

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