quast
clinker
| quast | clinker | |
|---|---|---|
| 1 | 2 | |
| 364 | 501 | |
| 1.9% | - | |
| 0.0 | 3.2 | |
| 8 months ago | 10 months ago | |
| AMPL | Python | |
| GNU General Public License v3.0 or later | MIT License |
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quast
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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.
clinker
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Need help with protein gene-neighborhood methods.
Being a silent reader all this while, this is my first question here and a very basic indeed. I want to generate some gene neighborhood clusters for a set of protein fasta files I have from UniProtKB. I plan to use: 1. http://www.webflags.se/ and 2. https://github.com/gamcil/clinker
- Stuck Running Bioinformatics Tool Through Command
What are some alternatives?
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
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
merqury - k-mer based assembly evaluation
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
CompareGenomeQualities - Reference free comparison of genome assemblies
pyGenomeViz - A genome visualization python package for comparative genomics
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report.
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
dash - Data Apps & Dashboards for Python. No JavaScript Required.