PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

Abstract

Motivation: The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI's sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and its unique strategy of encoding sequence data into color signals.Results: We present the mapping software, named PerM (Periodic Seed Mapping) that uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared with state-of-the-art programs. The data structure in PerM requires only 4.5 bytes per base to index the human genome, allowing entire genomes to be loaded to memory, while multiple processors simultaneously map reads to the reference. Weight maximized periodic seeds offer full sensitivity for up to three mismatches and high sensitivity for four and five mismatches while minimizing the number random hits per query, significantly speeding up the running time. Such sensitivity makes PerM a valuable mapping tool for SOLiD and Solexa reads.Availability: http://code.google.com/p/perm/Contact: tingchen@usc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Evaluation of next-generation sequencing software in mapping and assembly

“…The memory occupancy of these programs depends on the amount of reads that they processed, but it would be time consuming to scan the whole-genome when few reads are mapped. 25 Some programs such as BFAST, 28 Bowite, 20 BWA, 25 MOM, 29 MosaikAligner (http://bioinformatics.bc.edu/marthlab/ Mosaik), NovoAlign (http://www.novocraft.com), SOAP, 19 PASS, 18 PerM, 24 ProbeMatch, 30 SSAHA2, 31 index genomic sequence. This kind of software can easily be parallelized to work on multithreading at the cost of larger memory occupancy if the original genome is large such as the human genome sequence.…”

“…Quality scores that come with reads from NGS platforms (mainly from Illumina) are, arguably, crucial in preventing the possibility of trivial matches during the mapping. Most of the tools [18][19][20][21][22][23][24][25][26]28 available now use base quality information when they do mapping tasks, although some of them may not fully use it to advance mapping accuracy. However, there are also some programs, such as CloudBurst, SeqMap, MOM, ProbeMatch and Slider, that involve nucleotide information only for short reads alignment.…”

WALT: fast and accurate read mapping for bisulfite sequencing

“…WALT employs periodic spaced seeds, originally described by Chen et al (2009), to filter candidate mapping positions for each read. Three spaced seeds (010) *, 0(010) * and 00(010) * are used to guarantee full sensitivity for two mismatches (Supplementary Table S1 WALT converts all Cs in both the reads and the reference genome to Ts for mapping.…”

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

“…The hardware mapper is based on PerM [90], a software with periodic spaced seeds to significantly improve mapping efficiency for large reference genomes. Meshes of processing elements are implemented on Virtex-5 LX330 to take the advantage of the spatial parallelism on FPGA.…”