quast
bio-sequence
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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?
RNAlien - RNAlien - unsupervised RNA family model construction
BlastHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
cobot - Computational biology toolkit to collaborate with researchers in constructive protein engineering
Genbank - Genbank format tools and parser
bioinformatics-toolkit - A collection of bioinformatics algorithms
Biopython - Official git repository for Biopython (originally converted from CVS)
phybin - Binning (Newick) Phylogenetic Trees by Topology
FormalGrammars - Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)
ADPfusionForest - Dynamic programming on tree and forest structures
memexml - Haskell cabal libary for parsing Meme motif finder xml output
MutationOrder - most likely order of mutation events in RNA
EntrezHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice