JOURNAL ARTICLE

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads

Yun Heo, Xiao-Long Wu, Deming Chen, Jian Ma, Wen-Mei Hwu
Bioinformatics 2014 May 15, 30 (10): 1354-62
24451628

MOTIVATION: Rapid advances in next-generation sequencing (NGS) technology have led to exponential increase in the amount of genomic information. However, NGS reads contain far more errors than data from traditional sequencing methods, and downstream genomic analysis results can be improved by correcting the errors. Unfortunately, all the previous error correction methods required a large amount of memory, making it unsuitable to process reads from large genomes with commodity computers.

RESULTS: We present a novel algorithm that produces accurate correction results with much less memory compared with previous solutions. The algorithm, named BLoom-filter-based Error correction Solution for high-throughput Sequencing reads (BLESS), uses a single minimum-sized Bloom filter, and is also able to tolerate a higher false-positive rate, thus allowing us to correct errors with a 40× memory usage reduction on average compared with previous methods. Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads. Evaluations using real and simulated reads showed that BLESS could generate more accurate results than existing solutions. After errors were corrected using BLESS, 69% of initially unaligned reads could be aligned correctly. Additionally, de novo assembly results became 50% longer with 66% fewer assembly errors.

AVAILABILITY AND IMPLEMENTATION: Freely available at http://sourceforge.net/p/bless-ec

CONTACT: dchen@illinois.edu

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Full Text Links

Find Full Text Links for this Article

Discussion

You are not logged in. Sign Up or Log In to join the discussion.

Related Papers

Remove bar
Read by QxMD icon Read
24451628
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"