Tag: Aligner

BWA 0.7.17 – Burrows-Wheeler Aligner for Short and Long Reads.

BWA 0.7.17

:: DESCRIPTION

BWA (Burrows-Wheeler Aligner) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BWA

:: MORE INFORMATION

Citation:

Li H. and Durbin R. (2009)
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60.

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7 – Genome Aligner and Variant Caller

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7

:: DESCRIPTION

Isaac is ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. An ultrafast DNA sequence aligner /isaac_aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (isaac_variant_caller– Isaac Variant Caller) have been developed.

::DEVELOPER

Illumina, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Isaac

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):2041-3. doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.
Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW.

TopHat 2.1.1 – Short Read Aligner for RNA-Seq Experiments

TopHat 2.1.1

:: DESCRIPTION

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

TopHat

:: MORE INFORMATION

Citation

Trapnell C, Pachter L, Salzberg SL.
TopHat: discovering splice junctions with RNA-Seq.
Bioinformatics (2009) 25(9): 1105-1111.

Genome Biology 2013, 14:R36
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley and Steven L Salzberg

Bowtie 1.3.0 / Bowtie2 2.4.4 – Ultrafast Memory-efficient Short Read Aligner

Bowtie 1.3.0 / Bowtie2 2.4.4

:: DESCRIPTION

Bowtie is an ultrafast, memory-efficient short read aligner. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds.

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /Mac OsX

:: DOWNLOAD

Bowtie / Bowtie2

:: MORE INFORMATION

Citation

Langmead B, Trapnell C, Pop M, Salzberg SL.|
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biology 10:R25.

deBGA – de Bruijn Graph-based Aligner

deBGA

:: DESCRIPTION

deBGA is a seed-and-extension-based read alignment tool. It is suitable for aligning various kinds of high-throughput sequencing reads to multiple similar reference genomes.

::DEVELOPER

HIT Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 deBGA

:: MORE INFORMATION

Citation:

deBGA: read alignment with de Bruijn Graph-based seed and extension.
Liu B, Guo H, Brudno M, Wang Y.
Bioinformatics. 2016 Jul 4. pii: btw371.

sBWT 1.0b1 – Burrows–Wheeler transform (BWT) based Fast Indexer/Aligner

sBWT 1.0b1

:: DESCRIPTION

sBWT is a Burrows–Wheeler transform (BWT) based fast indexer/aligner specialized in parallelized indexing and searching for Next Generation Sequencing data.

::DEVELOPER

sBWT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 sBWT

:: MORE INFORMATION

Citation

sBWT: Memory Efficient Implementation of the Hardware-acceleration-friendly Schindler Transform for the Fast Biological Sequence Mapping.
Chang CH, Chou MT, Wu YC, Hong TW, Li YL, Yang CH, Hung JH.
Bioinformatics. 2016 Jul 13. pii: btw419.

CADBURE 20151031 – Evaluating Aligner performance on your RNA-Seq dataset

CADBURE 20151031

:: DESCRIPTION

The purpose of CADBURE (Comparing Alignment results of user Data Based on the relative reliability and advantage of Uniquely aligned REads) is to evaluate spliced aligner performance on user’s RNA-Seq data by comparing a pair of alignment results obtained either from two different aligners with the similar parameter set or from two different parameter sets with the same aligner.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CADBURE

:: MORE INFORMATION

Citation

Sci Rep. 2015 Aug 25;5:13443. doi: 10.1038/srep13443.
CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.
Kumar PK, Hoang TV, Robinson ML, Tsonis PA, Liang C

BIMA v3 – Aligner customized for Mate Pair Library Sequencing

BIMA v3

:: DESCRIPTION

BIMA is a mapping/alignment customized for mate-pair library next generation sequencing.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIMA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1627-9. doi: 10.1093/bioinformatics/btu078. Epub 2014 Feb 12.
BIMA V3: an aligner customized for mate pair library sequencing.
Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G.

BatAlign – A Short Read Aligner allowing Indels

BatAlign

:: DESCRIPTION

BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BatAlign

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 18;43(16):e107. doi: 10.1093/nar/gkv533.
BatAlign: an incremental method for accurate alignment of sequencing reads.
Lim JQ, Tennakoon C, Guan P, Sung WK.

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