Cassandra v15.4.10 – Combines Annovar Output with other Public Datasources to Output Annotated .vcf Files.

Cassandra v15.4.10

:: DESCRIPTION

Cassandra combines annovar output with other public datasources to output annotated .vcf files.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java
  • Perl
  • Annovar

:: DOWNLOAD

Cassandra

:: MORE INFORMATION

ReadTools 1.5.2 – Universal Toolkit for Handling Sequence data from different Sequencing Platforms

ReadTools 1.5.2

:: DESCRIPTION

ReadTools provides a consistent and highly tested set of tools for processing sequencing data from any kind of source and focusing on raw reads, while including tools for mapped reads as well.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

ReadTools

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2018 May;18(3):676-680. doi: 10.1111/1755-0998.12741. Epub 2017 Dec 8.
ReadTools: A universal toolkit for handling sequence data from different sequencing platforms.
Gómez-Sánchez D,SchlöttererÇ

ms2ms.pl – Convert the Output of Hudson’s Makesample software into Microsatellite data

ms2ms.pl

:: DESCRIPTION

ms2ms.pl converts the output of Hudson’s makesample software into microsatellite data. The output could be directly analyzed by MSA.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 ms2ms.pl

:: MORE INFORMATION

Citation

SREENIVASA R. PIDUGU andCHRISTIAN SCHLÖTTERER
ms2ms.pl: a PERL script for generating microsatellite data
Molecular Ecology Notes Volume 6, Issue 2, pages 580–581, June 2006

MINCE v0.5.0 ‐ Bucketing-based Reference-free Compression

MINCE v0.5.0

:: DESCRIPTION

MINCE is a technique for encoding collections of short reads so that they can be more effectively compressed via a standard compressor like LZIP.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

MINCE

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.
Data-dependent bucketing improves reference-free compression of sequencing reads.
Patro R, Kingsford C.

Referee – Rapid, Separable Compression for Sequence Alignments

Referee

:: DESCRIPTION

Referee is a command-line tool that takes sequence alignment SAM files and compresses them in a lossless manner.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Referee

:: MORE INFORMATION

Citation

Darya Filippova, Carl Kingsford (2015).
Rapid, separable compression enables fast analyses of sequence alignments.
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, pages 194-201.

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.

Phy2HTML 1.0 – Display Phylogeny using only HTML and CSS

Phy2HTML 1.0

:: DESCRIPTION

Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Phy2HTML

:: MORE INFORMATION

JPhyloIO 1.0.0 – Reading and Writing of different Phylogenetic File Formats

JPhyloIO 1.0.0

:: DESCRIPTION

JPhyloIO is an open source Java library for reading and writing phylogenetic file formats. The main aim is to provide access to various formats using a single interface, while being independent of the concrete application data model, to achieve maximal flexibility.

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

JPhyloIO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2019 Jul 22;20(1):402. doi: 10.1186/s12859-019-2982-3.
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface.
Stöver BC, Wiechers S, Müller KF.

tax2tree 1.0 – Decorating Taxonomy onto a Phylogenetic tree

tax2tree 1.0

:: DESCRIPTION

tax2tree is a tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python
  • PyCogent

:: DOWNLOAD

 tax2tree

:: MORE INFORMATION

Citation

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z DeSantis, Alexander Probst, Gary L Andersen, Rob Knight and Philip Hugenholtz.
ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.

NGC 0.0.1 – Compressor for High-throughput Sequencing data

NGC 0.0.1

:: DESCRIPTION

NGC is a compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.

::DEVELOPER

Niko Popitsch the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 NGC

:: MORE INFORMATION

Citation

Niko Popitsch and Arndt von Haeseler
NGC: lossless and lossy compression of aligned high-throughput sequencing data
Nucl. Acids Res. (7 January 2013) 41 (1): e27.