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Hello,
I'd like to start out by saying I really like Flye. It's great, and the latest improvements have been great.
I am however having some trouble with some of my trickier genome assembies.
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Hello,
Is it possible to profile contigs over reads?
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Dear Silas,
Last time, I consulted you about the taxonomic and functional profiling for metagenomic data. After check the several papers and blocks, I want to try metaphlan2 and humann2 to get taxo…
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Hi,
I have used checkm merger function produced the merger.tsv file. I have also looked at the paper published 'Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of…
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Hi, I just discovered this tool and find it very interesting.
I have whole genome metagenomic sequences from plant roots. I have assembled them into contigs. I used softwares like prokka/prodigal to…
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Hey @charlesreid1 and @brooksph , is this an accurate figure for the assembly workflow? This figure assumes that we’re using the MetaQUAST capability within QUAST and not using PANDAseq, and those ass…
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Hi Donovan,
I am trying to filter scaffolds following the methods presented on your paper (Parks DH et al. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree…
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We have a viral metagenome sequenced by 1D ligation and assembled in canu. Canu + PILON gets us within 99% ANI of contigs we see from SPAdes hybrid assemblies. I would like to try CANU + nanopolish + …
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Hi,
Have been playing around with sourmash and it seems to be quite a handy tool. However, I am having trouble making sense of the output data.
I ran sourmash gather with a metagenome assembled …
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I’m trying to use vg for metagenome analysis. As many assembled fragments have attached to the reference sequence with only in one end (and other terminal of the sequence has not determined), so I cre…