elPrep 2.4 – High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

elPrep  2.4

:: DESCRIPTION

elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.

::DEVELOPER

The Exascience Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 elPrep

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J

rMAPS v1.0.1 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS v1.0.1

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.

xMAN 20060925 – MAp OligoNucleotides to Subject Genome

xMAN 20060925

:: DESCRIPTION

xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.

::DEVELOPER

Xiaole Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  xMAN

:: MORE INFORMATION

Citation:

Li W, Carroll JS, Brown M, Liu S.
xMAN: extreme MApping of OligoNucleotides.
BMC Genomics. 2008;9 Suppl 1:S20.

tfbs_species 1.0 – Map Human Transcription Factor Binding Sites to Another Species

tfbs_species 1.0

:: DESCRIPTION

The aim of tfbs_species is to translate a list of binding sites from the University of California Santa Cruz(UCSC) Genome database from one species to another. At the moment, this data only exists for the human genome

::DEVELOPER

Raymond Wan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  tfbs_species

:: MORE INFORMATION

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

Medical information and systems biology laboratory, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.

MAPanalyzer – Analyzing Microtubule-associated Proteins

MAPanalyzer

:: DESCRIPTION

MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
Zhou Y, Yang S, Mao T, Zhang Z.
Database (Oxford). 2015 Nov 13;2015. pii: bav108. doi: 10.1093/database/bav108.

PDB-Explorer – Web-based interactive Map of PDB in Shape Space

PDB-Explorer

:: DESCRIPTION

PDB-Explorer is a web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.

::DEVELOPER

PDB-Explorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL.
BMC Bioinformatics. 2015 Oct 23;16(1):339.

PanGIA 3.0 – Analysis of Physical and Genetic Interactions to infer Genetic Module Maps

PanGIA 3.0

:: DESCRIPTION

PanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps.

::DEVELOPER

PanGIA team

:: SCREENSHOTS

PanGIA

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
:: DOWNLOAD

 PanGIA

:: MORE INFORMATION

Citation

F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.
Porting and using PanGIA for Cytoscape 3: challenges and solutions.
Welker D, Demchak B

GenGIS 2.4.0 – Combine Digital Map data with Genomic Data

GenGIS 2.4.0

:: DESCRIPTION

GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenGIS

:: MORE INFORMATION

Citation:

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009.
GenGIS: A geospatial information system for genomic data.
Genome Research, 19: 1896-1904

BirdsEyeView – Maps Experimental Data to Different Cell Compartments

BirdsEyeView

:: DESCRIPTION

BirdsEyeView is a Java application that maps experimental data to different cell compartments, pathways, and GO Ontology categories in order to give a “bird’s eye view” of the data.

::DEVELOPER

Lifeng Zhang (zlfpeak@iastate.edu)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

BirdsEyeView

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 15:S11. doi: 10.1186/1471-2105-13-S15-S11. Epub 2012 Sep 11.
BirdsEyeView (BEV): graphical overviews of experimental data.
Zhang L1, Berleant D, Wang Y, Li L, Cook D, Wurtele ES.