quast
too-many-cells
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| quast | too-many-cells | |
|---|---|---|
| 1 | - | |
| 361 | 100 | |
| 2.8% | - | |
| 0.0 | 4.5 | |
| 8 months ago | 5 months ago | |
| AMPL | Haskell | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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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.
too-many-cells
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Tracking mentions began in Dec 2020.
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
subsample - Subsample data from a uniform distribution so two different statuses for the same entity have the same number of samples.
merqury - k-mer based assembly evaluation
collapse-duplication - Process the output of heatitup in order to collapse sequences into clones by similar ITD mutations.
CompareGenomeQualities - Reference free comparison of genome assemblies
integreat - Integrate difference data sources and optionally perform differential integration.
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
normalize - normalize
clinker - Gene cluster comparison figure generator
heatitup-complete - Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion. A layer on top of heatitup for additional functionality such as working with BAM files directly.
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
tex-join-bib - Compile separate tex files with the same bibliography.