Tag: Plasmids

Deeplasmid – Identifying Plasmids in Microbial Isolates and Assembled Metagenomes

Deeplasmid

:: DESCRIPTION

Deeplasmid is a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data.

::DEVELOPER

Deeplasmid team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

Deeplasmid

:: MORE INFORMATION

Citation

Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A.
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.
Nucleic Acids Res. 2021 Dec 6:gkab1115. doi: 10.1093/nar/gkab1115. Epub ahead of print. PMID: 34871418.

Recycler v0.7 – Detecting Plasmids from de novo Assembly Graphs

Recycler v0.7

:: DESCRIPTION

Recycler is a tool for extracting cyclical sequences from assembly graphs that are likely to be plasmids, phages, or other mobile elements that are physically separate from their host genomes. It can be applied on isolate, metagenome, and plasmidome graphs.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Recycler

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):475-482. doi: 10.1093/bioinformatics/btw651.
Recycler: an algorithm for detecting plasmids from de novo assembly graphs.
Rozov R, Brown Kav A, Bogumil D, Shterzer N, Halperin E, Mizrahi I, Shamir R.