PGA VS BBMap

Compare PGA vs BBMap and see what are their differences.

PGA

Plastid Genome Annotator (by quxiaojian)
chloroplast plastid plastome Genome Annotation
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BBMap

(Not Offical) BBMap short read aligner, and other bioinformatic tools. (by BioInfoTools)
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PGA BBMap
1 1
46 115
- -
0.0 1.4
over 3 years ago over 3 years ago
Perl Java
GNU General Public License v3.0 only GNU General Public License v3.0 or later
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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PGA

Posts with mentions or reviews of PGA. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-03-04.
  • Extracting CDS from fragmented assemblies
    2 projects | /r/bioinformatics | 4 Mar 2021
    The tool PGA was recommended to me for annotation the assemblies, but it will not accept a multifasta as input. I have to "fuse" the contigs somehow for this tool to work, which I've tried to do a couple different ways described below. Once I have assemblies with just a single sequence, I have no problems annotating them and getting the extracted CDS.

BBMap

Posts with mentions or reviews of BBMap. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-03-04.
  • Extracting CDS from fragmented assemblies
    2 projects | /r/bioinformatics | 4 Mar 2021
    I used minimap2 to align the contigs to the reference, then extract them in the correct order (I've also tried mauve contig mover for this). Once I get the contigs in the correct order, I use BBmap fuse.sh to "fuse" the contigs in the correct order. This script has the ability to add a given number of "Ns" in between each fused contig. I chose to add 5 between each contig.

What are some alternatives?

When comparing PGA and BBMap you can also consider the following projects:

Augustus - Genome annotation with AUGUSTUS

label-studio - Label Studio is a multi-type data labeling and annotation tool with standardized output format

PGA vs Augustus PGA vs label-studio