Tag: Recovery

DAS tool 1.1.3 – Recovery of Genomes from Metagenomes via Dereplication, Aggregation, and Scoring Strategy

DAS tool 1.1.3

:: DESCRIPTION

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

DAS Tool

:: MORE INFORMATION

Citation

Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF.
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.
Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28. PMID: 29807988; PMCID: PMC6786971.

FACTERA 1.3 – Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm

FACTERA 1.3

:: DESCRIPTION

FACTERA is a tool for practical and robust de novo enumeration of genomic fusions and breakpoints from paired-end targeted (or genome-wide) sequencing data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FACTERA

:: MORE INFORMATION

Citation

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
Newman AM, Bratman SV, Stehr H, Lee LJ, Liu CL, Diehn M, Alizadeh AA.
Bioinformatics. 2014 Aug 20. pii: btu549.

RecoverY – Classification of Y-chromosome Specific Reads

RecoverY

:: DESCRIPTION

RecoverY is a tool for shortlisting enriched reads from a sequencing dataset, based on k-mer abundance. Specifically, it can be used for isolating Y-specific reads from a Y flow-sorted dataset.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RecoverY

:: MORE INFORMATION

Citation:

Bioinformatics, 34 (7), 1125-1131 2018 Apr 1
RecoverY : k-mer-based read classification for Y-chromosome-specific sequencing and assembly,
Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna Makova, Paul Medvedev