Abstract
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of k-mer length, the key parameter of k-spectrum-based family of correctors. The correction algorithms are examined on huge data sets, i.e., human and maize genomes for both Illumina HiSeq and MiSeq instruments.
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Acknowledgements
The work was supported by the Polish National Science Center upon decision DEC-2015/17/B/ST6/01890.
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Appendix
Appendix
To generate reads we placed a real source profile in a directory profile_dir and run read Art with the following commands:
art_profiler_illumina<profile_name><profile_dir>/ fastq
art_illumina -sam -1<profile_name> -l<read_length> -i<genome> -c<read_number> -o<output> -rs 0 -na
We run correctors with the following commands with the parameters specified in Table 2:
reckoner -kmerlength<k> -prefix .<input_file>
bless -read<input_file> -kmerlength<k> -prefix tmp -gzip
bfc -s<genome_size> -t 64<input_file>><output_file>
musket -k<k><kmers> -p 64 -o<output_file><input_file>
Sizes of the correctors input data is presented in Table 3.
We run assembly with Minia (version 2.0.3) with the following command:
minia -in<input_file> -abundance-min 2 -max-memory 204800 -out
<output_con_file>
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Długosz, M., Deorowicz, S., Kokot, M. (2018). Improvements in DNA Reads Correction. In: Gruca, A., Czachórski, T., Harezlak, K., Kozielski, S., Piotrowska, A. (eds) Man-Machine Interactions 5. ICMMI 2017. Advances in Intelligent Systems and Computing, vol 659. Springer, Cham. https://doi.org/10.1007/978-3-319-67792-7_12
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