MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates. (by bhattlab)
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes (by tseemann)
| MGEfinder | abricate | |
|---|---|---|
| 1 | 3 | |
| 99 | 343 | |
| - | - | |
| 0.0 | 0.0 | |
| 8 months ago | 6 months ago | |
| Python | Perl | |
| MIT License | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
MGEfinder
Posts with mentions or reviews of MGEfinder.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-03-25.
-
Predicting Antimicrobial Resistance in a Sequence
To identify MGE’s you could try: https://github.com/bhattlab/MGEfinder
abricate
Posts with mentions or reviews of abricate.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-03-25.
- Predicting Antimicrobial Resistance in a Sequence
-
best way to identify AMR genes from a whole genome
I personally use ABRicate because it's simple https://github.com/tseemann/abricate. But there's a whole heap of other tools and papers like this commenting on those https://www.frontiersin.org/articles/10.3389/fpubh.2019.00242/full
-
best way to search whole genomes for known antibiotics resistance genes
Try abricate https://github.com/tseemann/abricate
What are some alternatives?
When comparing MGEfinder and abricate you can also consider the following projects:
ariba - Antimicrobial Resistance Identification By Assembly
abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes