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

Blue 1.1.3 – Short-read Error-correction tool

Blue 1.1.3

:: DESCRIPTION

Blue is a fast, accurate short-read error-correction tool based on k-mer consensus and context. It will correct both Illumina and 454-like data, and accepts sequence data files in both FASTQ and FASTA formats.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Blue

:: MORE INFORMATION

Citation

Blue: correcting sequencing errors using consensus and context.
Greenfield P, Duesing K, Papanicolaou A, Bauer DC.
Bioinformatics. 2014 Jun 11. pii: btu368.

AREM 1.0.1 – Aligning Short Reads from ChIP-sequencing by Expectation Maximization

AREM 1.0.1

:: DESCRIPTION

AREM (Aligning reads by Expectation-Maximization) is a peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  AREM

:: MORE INFORMATION

Citation:

J Comput Biol. 2011 Nov;18(11):1495-505. Epub 2011 Oct 28.
AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.

Illuminator 20110419 – Mutation Detection using Short-read Clonal Sequencing

Illuminator 20110419

:: DESCRIPTION

Illuminator is a new sequence alignment program for the output from Illumina GA-II clonal sequencers. It is aimed primarily at kilobase-sized reference regions, as would typically be used in the context of mutation detection.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 Illuminator

:: MORE INFORMATION

Citation

Carr IM, Morgan JE, Diggle CP, Sheridan EG, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT.
Illuminator, a desktop program for mutation detection using short-read clonal sequencing.
Genomics 2011 Oct;98(4):302-9.

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

ngs-bits 2021_03 – Short-read sequencing tools

ngs-bits 2021_03

:: DESCRIPTION

ngs-bits is a collection of tools for short-read data analysis.

::DEVELOPER

Arbeitsgruppe Genomik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Bioconda

:: DOWNLOAD

ngs-bits

:: MORE INFORMATION

Citation

Schroeder CM, Hilke FJ, Löffler MW, Bitzer M, Lenz F, Sturm M.
A comprehensive quality control workflow for paired tumor-normal NGS experiments.
Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032. PMID: 28130233.

LoQuM 0.2 – LOgistic Regression tool for Calibrating the QUality of Short Read Mappings

LoQuM 0.2

:: DESCRIPTION

LoQuM assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool.

::DEVELOPER

LoQuM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • R

:: DOWNLOAD

 LoQuM

:: MORE INFORMATION

Citation

Accurate estimation of short read mapping quality for next-generation genome sequencing.
Ruffalo M, Koyutürk M, Ray S, LaFramboise T.
Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

ShoRAH v1.9.95 – Short Reads Assembly into Haplotypes

ShoRAH v1.9.95

:: DESCRIPTION

ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShoRAH

:: MORE INFORMATION

Citation

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinformatics, vol. 12 p. 119

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.