Centrifuge 1.0.4-beta – Classifier for Metagenomic Sequences

Centrifuge 1.0.4-beta

:: DESCRIPTION

Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Centrifuge

:: MORE INFORMATION

Diamund – DIrect Alignment for MUtatioN Discovery

Diamund

:: DESCRIPTION

Diamund is a new, efficient algorithm for variant detection that compares DNA sequences directly to one another, without aligning them to the reference genome.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Diamund

:: MORE INFORMATION

Citation

Hum Mutat. 2014 Mar;35(3):283-8. doi: 10.1002/humu.22503.
DIAMUND: direct comparison of genomes to detect mutations.
Salzberg SL, Pertea M, Fahrner JA, Sobreira N.

HISAT / HISAT2 2.1.0 – Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT / HISAT2 2.1.0

:: DESCRIPTION

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads.

HISAT2 is a successor to both HISAT and TopHat2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 HISAT2

:: MORE INFORMATION

Citation

HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL.
Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317.

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.

dmatch 0.1.8 – Alignment of single-cell RNA-seq samples using Density Matching

dmatch 0.1.8

:: DESCRIPTION

Dmatch is a method that leverages an external expression atlas of human primary cells and kernel density matching to align multiple scRNA-seq experiments for downstream biological analysis.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX

:: DOWNLOAD

Dmatch

:: MORE INFORMATION

Citation

Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li YI.
Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Genome Res. 2021 Apr;31(4):698-712. doi: 10.1101/gr.261115.120. Epub 2021 Mar 19. PMID: 33741686; PMCID: PMC8015859.

PEANUT 1.3.7 – The ParallEl AligNment UTility

PEANUT 1.3.7

:: DESCRIPTION

PEANUT is a read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

  PEANUT

:: MORE INFORMATION

Citation

Köster J, Rahmann S (2014).
Massively parallel read mapping on GPUs with the q-group index and PEANUT.
PeerJ 2:e606 http://dx.doi.org/10.7717/peerj.606

Alfred v0.2.3 – BAM Alignment Statistics, Feature Counting and Annotation

Alfred v0.2.3

:: DESCRIPTION

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments

::DEVELOPER

Tobias Rausch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alfred

:: MORE INFORMATION

Citation:

Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.

Wasabi 20200205 – Powerful Multiple Sequence Alignment Browser

Wasabi 20200205

:: DESCRIPTION

Wasabi is a tool for visualisation and manipulation of rich MSAs and a graphical interface to command-line programs.

::DEVELOPER

Löytynoja Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • Java

:: DOWNLOAD

 Wasabi

:: MORE INFORMATION

Citation

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
Veidenberg A, Medlar A, Löytynoja A.
Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333.

CHAIN 1.0.0 – Forging Evolutionary Links to Underlying Mechanisms

CHAIN 1.0.0

:: DESCRIPTION

Many important principles underlying how protein molecular machines work lie beyond the pale of direct experimental observation. CHAIN (Contrast Hierarchical Alignment and Interaction Network )  analysis is a statistical solution to this problem that follows Mendel’s example: Just as Mendel inferred principles underlying genetic mechanisms from observed patterns of inherited traits, CHAIN analysis seeks to infer principles underlying molecular mechanisms from observed patterns in protein sequences—the cell’s own language for encoding those mechanisms.

::DEVELOPER

Andrew F. Neuwald, Ph.D.

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHAIN

:: MORE INFORMATION

Citation

Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.
The CHAIN program: forging evolutionary links to underlying mechanisms.
Neuwald AF

GISMO 2.0 – Gibbs Sampler for Multi-alignment Optimization

GISMO 2.0

:: DESCRIPTION

GISMO is a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA)

::DEVELOPER

GISMO team

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISMO

:: MORE INFORMATION

Citation

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald AF, Altschul SF.
PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936.