lapels 1.0.7 – Remapper and Annotator of in silico (pseudo) Genome Alignments

lapels 1.0.7

:: DESCRIPTION

Lapels is used to remap in silico (pseudo) genome alignments, in the form of a BAM file, back to the reference sequence. This entails the removal of all indels (via the cigar string modifications, the underlying sequence is unaltered) and adjustment fragment and mate starting positions. Lapels also annotates the number and types (SNPs, insertions, and deletions) of allele variants seen in each read.

::DEVELOPER

Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 lapels

:: MORE INFORMATION

GenMAPP-CS 0.2 – GenMAPP Pathway Analysis and Visualization in Cytoscape

GenMAPP-CS 0.2

:: DESCRIPTION

GenMAPP-CS is open-source software for pathway visualization and analysis, bringing the intuitive and easy-to-use features of GenMAPP to the powerful and flexible Cytoscape platform

::DEVELOPER

the Conklin Lab at the Gladstone Institutes at theUniversity of California at San Francisco

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenMAPP-CS

:: MORE INFORMATION

Citation

Salomonis, K Hanspers, AC Zambon, K Vranizan, SC Lawlor, KD Dahlquist, SW Doniger, J Stuart, BR Conklin, and AR Pico. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics, Jun 2007; 8: 217
[PMID: 17588266]

RAREVATOR – RAre REference VAriant annotaTOR

RAREVATOR

:: DESCRIPTION

RAREVATOR is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data.

::DEVELOPER

RAREVATOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAREVATOR

:: MORE INFORMATION

Citation:

Characterization and identification of hidden rare variants in the human genome
Magi A, D’Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF.
BMC Genomics. 2015 Apr 24;16(1):340.

VANO 1.741 – 3D Image Annotator

VANO 1.741

:: DESCRIPTION

VANO (Volume-object annotation system) is a System for 3D multicolor image stacks. VANO provides a well-coordinated way to annotate hundreds or thousands of 3D image objects. It combines 3D views of images and spread sheet neatly, and is just easy to manage 3D segmented image objects.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

VANO

:: MORE INFORMATION

Citation:

Peng, H., Long, F., Myers, E.W.,
VANO: a volume-object image annotation system,”
Bioinformatics, Vol. 25, No. 5, pp. 695-697, 2009.