As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

/pdf/fast-gapped-read-alignment-with-bowtie-2-2axet5ses2.pdf

Fast gapped-read alignment with Bowtie 2

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

/pdf/spades-a-new-genome-assembly-algorithm-and-its-applications-35zec7ea02.pdf

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.

Fast and sensitive protein alignment using DIAMOND

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Summary: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures. Availability: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/. Contact: shrimp@cs.toronto.edu Supplementary information: Supplementary data are available at Bioinformatics online.

/pdf/shrimp2-sensitive-yet-practical-short-read-mapping-32q2s63sks.pdf

SHRiMP2: Sensitive yet Practical Short Read Mapping

Motivation: High-throughput sequencing technologies produce very large amounts of data and sequencing errors constitute one of the major problems in analyzing such data. Current algorithms for correcting these errors are not very accurate and do not automatically adapt to the given data. Results: We present HiTEC, an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods. Our approach provides significantly higher accuracy than previous methods. It is time and space efficient and works very well for all read lengths, genome sizes and coverage levels. Availability: The source code of HiTEC is freely available at www.csd.uwo.ca/~ilie/HiTEC/. Contact: ilie@csd.uwo.ca

/pdf/hitec-accurate-error-correction-in-high-throughput-48owe2zned.pdf

HiTEC: accurate error correction in high-throughput sequencing data

We give two new algorithms for constructing small nondeterministic finite automata (NFA) from regular expressions. The first constructs NFAs with e-transitions (eNFA) which are smaller than all the other eNFAs obtained by similar constructions. Their size is at most 3/2 |α| + 5/2, where α is the regular expression. This is very close to optimal since we prove also the lower bound 4/3; |α| + 5/2. The second constructs NFAs. It uses e-elimination in the eNFAs we just introduced and builds a quotient of the well-known position automaton w.r.t. the equivalence given by the follow relation; therefore giving the name of follow automaton. The new automaton uses optimally the information from the positions of a regular expression. We compare the follow automaton with the best constructions to date and show that it has important advantages over those.

Follow automata

https://hal-upec-upem.archives-ouvertes.fr/hal-00619691/document

Computing Longest Previous Factor in linear time and applications

Motivation: High-throughput next-generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications. The quality of the sequencing data is crucial for all applications. A significant portion of the data produced contains errors, and ever more efficient error correction programs are needed. Results: We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data. RACER has better error-correcting performance than existing programs, is faster and requires less memory. To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets. Availability: RACER is freely available for non-commercial use at www.csd.uwo.ca/� ilie/RACER/. Contact: ilie@csd.uwo.ca Supplementary information: Supplementary data are available at Bioinformatics online.

/pdf/racer-rapid-and-accurate-correction-of-errors-in-reads-1lt83337h0.pdf

Lucian Ilie

Papers

SHRiMP2: Sensitive yet Practical Short Read Mapping

HiTEC: accurate error correction in high-throughput sequencing data

Follow automata

Computing Longest Previous Factor in linear time and applications

RACER: Rapid and accurate correction of errors in reads.