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.

RESCRIPt 2021.8.0 – REference Sequence annotation and CuRatIon Pipeline

RESCRIPt 2021.8.0

:: DESCRIPTION

RESCRIPt is a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases.

::DEVELOPER

Laboratory of Food Systems Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python
  • QIIME
  • conda

:: DOWNLOAD

RESCRIPt

:: MORE INFORMATION

Citation:

Robeson MS 2nd, O’Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA.
RESCRIPt: Reproducible sequence taxonomy reference database management.
PLoS Comput Biol. 2021 Nov 8;17(11):e1009581. doi: 10.1371/journal.pcbi.1009581. Epub ahead of print. PMID: 34748542.

Canto v1651 – Community Literature Curation

Canto v1651

:: 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

:: 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.

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