Arioc 1.43 – High-throughput Read Alignment with GPU-accelerated Exploration of Seed-and-extend Search Space

Arioc 1.43

:: DESCRIPTION

Arioc is a set of computer programs that carry out the alignment of short DNA sequences to a comparatively large reference sequence or genome.

::DEVELOPER

Arioc team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Arioc

:: MORE INFORMATION

Citation

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.
Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS.
PeerJ. 2015 Mar 3;3:e808. doi: 10.7717/peerj.808. eCollection 2015.

ArchAlign 1.5 – Chromatin Alignment Algorithm for Detecting Chromatin Architecture

ArchAlign 1.5

:: DESCRIPTION

ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets, derived from next-generation sequencing or tiled microarray approaches, by aligning chromatin signals for regions of interest.

::DEVELOPER

Buck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ArchAlign

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(12):R126. doi: 10.1186/gb-2010-11-12-r126. Epub 2010 Dec 23.
ArchAlign: coordinate-free chromatin alignment reveals novel architectures.
Lai WK1, Buck MJ.

FastSP 1.6.0 – Calculation of Alignment Accuracy

FastSP 1.6.0

:: DESCRIPTION

FastSP is a Java program for computing alignment error (SP-FN) quickly and using little memory.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Java

:: DOWNLOAD

  FastSP

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 1;27(23):3250-8. doi: 10.1093/bioinformatics/btr553. Epub 2011 Oct 7.
FastSP: linear time calculation of alignment accuracy.
Mirarab S1, Warnow T.

UPP – Ultra-large alignments using Phylogeny-aware Profiles

UPP

:: DESCRIPTION

UPP addresses the problem of alignment of very large datasets, potentially containing fragmentary data.

::DEVELOPER

Siavash Mirarab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python

:: DOWNLOAD

 UPP

:: MORE INFORMATION

Citation

Ultra-large alignments using phylogeny-aware profiles.
Nguyen NP, Mirarab S, Kumar K, Warnow T.
Genome Biol. 2015 Jun 16;16(1):124.

SATé 2.2.7 – Simultaneous Alignment and Tree Estimation

SATé 2.2.7

:: DESCRIPTION

SATé is a software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data set is divided into smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged for phylogenetic tree inference.

::DEVELOPER

The Holder Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SATé

:: MORE INFORMATION

Citation:

Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder.
SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees.”
Systematic Biology. 61(1):90-106

PconsC – Combination of Direct Information methods and Alignments improves Contact Prediction

PconsC

:: DESCRIPTION

PconsC is a software of combination of direct information methods and alignments improves contact prediction.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

  PconsC

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1815-6. doi: 10.1093/bioinformatics/btt259. Epub 2013 May 8.
PconsC: combination of direct information methods and alignments improves contact prediction.
Skwark MJ1, Abdel-Rehim A, Elofsson A.

TRACE-RRBS v0.1 – Targeted Alignment and Artificial Cytosine Elimination for RRBS

TRACE-RRBS v0.1

:: DESCRIPTION

TRACE-RRBS is a full pipeline for mapping bisulfite se-quencing data using bowtie2 and then generating CpG level data.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox

:: DOWNLOAD

 TRACE-RRBS

:: MORE INFORMATION

Citation

Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data.
Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z.
BMC Genomics. 2016 Feb 27;17(1):149. doi: 10.1186/s12864-016-2494-8.

PASsiT 1.0 – Post Alignment SNV Tools

PASsiT 1.0

:: DESCRIPTION

PASsiT (Post Alignment SNV Tools) is a suite of tools developed to help in our high-throughput sequencing and analysis environment.With single nucleotide variations (SNVs) being identified in ever increasing numbers with next generation sequencing data, we are often interested in a breakdown of the effect of the mutations, and if a particular change is somatic or germline. We are also interested in high quality true positive mutations, which are increasingly important considering their use in clinical decisions.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASsiT

:: MORE INFORMATION

See poster presented at RECOMB 2011 for more details:
http://www.bcgsc.ca/downloads/passit/PASsiT.pdf

DIDA 1.0.1 – Distributed and Parallel Indexing and Alignment algorithm

DIDA 1.0.1

:: DESCRIPTION

DIDA is a novel framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  DIDA

:: MORE INFORMATION

Citation

DIDA: Distributed Indexing Dispatched Alignment.
Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I.
PLoS One. 2015 Apr 29;10(4):e0126409. doi: 10.1371/journal.pone.0126409.

XMatchView 1.2.5 – Visualize DNA Sequence Alignments.

XMatchView 1.2.5

:: DESCRIPTION

XMatchView is a python application designed to visualize DNA sequence alignments.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 XMatchView

:: MORE INFORMATION