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.

SHORE 0.9.3 – Analysis Suite for Illumina Short Read Data

SHORE 0.9.3

:: DESCRIPTION

SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHORE

:: MORE INFORMATION

Citation

Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

GenomeMapper 0.4.4 – Short Read Mapping tool

GenomeMapper 0.4.4

:: DESCRIPTION

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter.

:DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 GenomeMapper

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(9):R98. Epub 2009 Sep 17.
Simultaneous alignment of short reads against multiple genomes.
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

MICA-aligner r345 – Next-generation sequencing short reads aligner based on Intel MIC

MICA-aligner r345

:: DESCRIPTION

MICA-aligner is a new short-read aligner that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core.

::DEVELOPER

MICA-aligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MICA-aligner

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Apr 23;16 Suppl 7:S10. doi: 10.1186/1471-2105-16-S7-S10. Epub 2015 Apr 23.
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).
Luo R, Cheung J, Wu E, Wang H, Chan SH, Law WC, He G, Yu C, Liu CM, Zhou D, Li Y, Li R, Wang J, Zhu X, Peng S, Lam TW.

ngsShoRT 2.2 – A Next Generation Sequencing Short Read Trimmer

ngsShoRT 2.2

:: DESCRIPTION

ngsShoRT algorithms are designed to pre-process Single Read (SR) or Paired-end (PE)/Mate-pair (MP) reads in FastQ format or Illumina’s native QSEQ format (with compressed file support). It privides parallel processing by multi-threading to deal with large volume of data and reduce running time. Another unique feature of ngsShoRT is that it was designed to handle PE/MP reads generically using paired-end specific modules.

::DEVELOPER

ngsShoRT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ngsShoRT

:: MORE INFORMATION

Citation

Software for pre-processing Illumina next-generation sequencing short read sequences.
Chen C, Khaleel SS, Huang H, Wu CH.
Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8

Kpath 0.6.3 – Statistical Reference-based Compression for Short Reads

Kpath 0.6.3

:: DESCRIPTION

Kpath (PathEnc) is a reference-based compression software of short read data sets.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Go

:: DOWNLOAD

 Kpath

:: MORE INFORMATION

Citation

Reference-based compression of short-read sequences using path encoding.
Kingsford C, Patro R.
Bioinformatics. 2015 Feb 2. pii: btv071.

GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9 – Pairwise Short-read Alignment

GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9

:: DESCRIPTION

GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps.

GapMis is a tool for pairwise sequence alignment with a single gap.

GapMis-OMP is the OpenMP-based version of GapMis.

libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • EMBOSS
  • Python
  • C Compiler

:: DOWNLOAD

 GapsMisGapMis , GapMis-OMP , libgapmis 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.
libgapmis: extending short-read alignments.
Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.
Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.

Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler.
Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library

InteMAP 1.0 – Integrated Metagenomic Assembly pipeline for NGS Short Reads

InteMAP 1.0

:: DESCRIPTION

InteMAP is a pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  InteMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.
Lai B, Wang F, Wang X, Duan L, Zhu H

ShotGun 1.0.10 – Flexible Short Read Simulator

ShotGun 1.0.10

:: DESCRIPTION

ShotGun is a flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth distribution to be either the ideal Poisson or Negative Binomial to model the overdispersion observed with real sequencing data. In addition, ShotGun performs computationally efficient Single Nucleotide Polymorphism (SNP) discovery using a statistic aggregated across all sequenced samples. False positives can be controlled at any desired rate according to the null distribution of this multi-sample statistic.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 ShotGun

:: MORE INFORMATION