JOURNAL ARTICLE
REVIEW

Sequence assembly using next generation sequencing data—challenges and solutions

Francis Y L Chin, Henry C M Leung, S M Yiu
Science China. Life Sciences 2014, 57 (11): 1140-8
25326069
Sequence assembling is an important step for bioinformatics study. With the help of next generation sequencing (NGS) technology, high throughput DNA fragment (reads) can be randomly sampled from DNA or RNA molecular sequence. However, as the positions of reads being sampled are unknown, assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence. Compared with traditional Sanger sequencing methods, although the throughput of NGS reads increases, the read length is shorter and the error rate is higher. It introduces several problems in assembling. Moreover, paired-end reads instead of single-end reads can be sampled which contain more information. The existing assemblers cannot fully utilize this information and fails to assemble longer contigs. In this article, we will revisit the major problems of assembling NGS reads on genomic, transcriptomic, metagenomic and metatranscriptomic data. We will also describe our IDBA package for solving these problems. IDBA package has adopted several novel ideas in assembling, including using multiple k, local assembling and progressive depth removal. Compared with existence assemblers, IDBA has better performance on many simulated and real sequencing datasets.

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
25326069
×

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"