quast
bio-sequence
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| quast | bio-sequence | |
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| 1 | - | |
| 364 | - | |
| 3.6% | - | |
| 0.0 | - | |
| 8 months ago | - | |
| AMPL | ||
| GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" 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.
bio-sequence
We haven't tracked posts mentioning bio-sequence yet.
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
RNAlien - RNAlien - unsupervised RNA family model construction
merqury - k-mer based assembly evaluation
BlastHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
CompareGenomeQualities - Reference free comparison of genome assemblies
cobot - Computational biology toolkit to collaborate with researchers in constructive protein engineering
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Genbank - Genbank format tools and parser
clinker - Gene cluster comparison figure generator
bioinformatics-toolkit - A collection of bioinformatics algorithms
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Biopython - Official git repository for Biopython (originally converted from CVS)