DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files) (by Edinburgh-Genome-Foundry)
quast
Genome assembly evaluation tool (by ablab)
| DnaFeaturesViewer | quast | |
|---|---|---|
| 2 | 1 | |
| 547 | 364 | |
| 2.0% | 1.9% | |
| 5.9 | 0.0 | |
| 6 months ago | 8 months ago | |
| Python | AMPL | |
| MIT License | 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.
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.
DnaFeaturesViewer
Posts with mentions or reviews of DnaFeaturesViewer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-10.
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Software to make in-scale illustrations of genomic locations
If you can build a Python environment and do a little coding, DnaFeaturesViewer or pyGenomeViz would be good choices. You can generate the following figure from a Genbank file with about 10 lines of code. Of course, you can specify the range of coordinates to be plotted.
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pyGenomeViz: A genome visualization python package for comparative genomics
If you need to display annotations/genes within a single genome, DnaFeaturesViewer may be another good option.
quast
Posts with mentions or reviews of quast.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-10-01.
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Deciding on genome assembly software
Have you looked into QUAST for comparison of assemblies? How big is the bacterial community? You may need to do some binning of your contigs to separate them into species specific genomes. I can suggest metaGEM (developed by me! should be online in NAR any day now) for generating MAGs for your bacterial species. Although it currently only supports short reads, it may give you an idea of what the bacterial community looks like. Maybe also look into EukCC for estimating fungal genome completeness and/or EukRep for splitting the contigs according to prokaryotic/eukaryotic provenance. You could also try estimating community composition directly from short read analysis using e.g. mOTUs2, kraken/braken, metaphlan, etc.
What are some alternatives?
When comparing DnaFeaturesViewer and quast you can also consider the following projects:
pyGenomeViz - A genome visualization python package for comparative genomics
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
gggenomes - A grammar of graphics for comparative genomics
merqury - k-mer based assembly evaluation
CompareGenomeQualities - Reference free comparison of genome assemblies
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
clinker - Gene cluster comparison figure generator
EukCC - Tool to estimate genome quality of microbial eukaryotes