SV-plaudit – Structural Variant Image Curation and Analysis

SV-plaudit

:: DESCRIPTION

SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. SV-plaudit supports image generation sequencing data from BAM or CRAM files from Illumina paired-end sequencing, PacBio or Oxford Nanopore Technologies long-read sequencing, or 10X Genomics linked-read sequencing.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SV-plaudit

:: MORE INFORMATION

Citation:

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.
SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.
Belyeu JR et al.

Duphold v0.2.1 – Annotation and Curation of high-confidence Structural Variant Calls

Duphold v0.2.1

:: DESCRIPTION

Duphold (uphold your DUP and DEL calls) is a new method to efficiently annotate SV calls with sequence depth information that can add (or remove) confidence to SVs that are predicted to affect copy number.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Duphold

:: MORE INFORMATION

Citation:

Gigascience. 2019 Apr 1;8(4). pii: giz040. doi: 10.1093/gigascience/giz040.
Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls.
Pedersen BS, Quinlan AR

Canto v840 – Community Literature Curation

Canto v840

:: DESCRIPTION

Canto is an online annotation tool which has been developed to allow researchers to curate the genetic and molecular data from their publications for inclusion in public biological databases.

::DEVELOPER

Val Wood, Cambridge Systems Biology Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • GCC
  • CLucene

:: DOWNLOAD

 Canto

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 12.
Canto: an online tool for community literature curation.
Rutherford KM1, Harris MA, Lock A, Oliver SG, Wood V.

PubSearch 0.8.1 – Literature Curation Management System

PubSearch 0.8.1

:: DESCRIPTION

PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation.

::DEVELOPER

PubSearch Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PubSearch

:: MORE INFORMATION

Citation

Yoo, D, Xu, I, Berardini, T, Rhee, S, Narayanasamy, V, Twigger, S (2006)
PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature..
Curr Protoc Bioinformatics. 2006 Mar;Chapter 9:Unit9.7.