HOME
CV
RESEARCH
SOFTWARE
PUBLICATIONS
LAB
TEACHING
Correcting Illumina data
This page contains the programs used for evaluating the quality of error correction in Illumina data reported in the paper "Correcting Illumina data" by Michael Molnar and Lucian Ilie:
- readSearch.zip (program for searching whole reads)
- kmerSearch.zip (program for searching k-mers)
- scripts_running.zip (scripts for downloading the datasets used in the paper and running the error correcting programs: BLESS, Coral, HiTEC, Musket, RACER, SGA, SHREC)
- scripts_searching.zip (scripts for downloading the reference genome sequences and running readSearch and kmerSearch)
It is assumed that the user has properly installed the error correction programs and has them listed in their PATH. For downloading and extracting the datasets and genome sequences the user will need to have installed wget, cat, gunzip, fastq-dump (part of the NCBI Toolkit), and perl for the shuffleSequences_fastq.pl script (from the Velvet package).
July 22, 2014
© 2014 Michael Molnar, Lucian Ilie
contact: ilie@csd.uwo.ca