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Hello,
I am currently running 'medaka 0.8.1' with the following command line:
'medaka_consensus -i ./../barcode04_C251.fastq.gz -d C251_racon1.fasta -o C251_medaka_results -m r941_min_high'
…
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Per discussion here: https://sd2e.slack.com/archives/C5W4Y826Q/p1549579295335000
@dvnstrcklnd would like to:
"Find strains and plasmids from YS and audit them"
e.g. "I want to find all strain…
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Dear community,
I would like to ask how to know which step the canu is working? Is that possible to roughly estimate the time left canu run for read correction?
So far I saw the ```Crystal_all_1…
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Hi,
Thank you for Ra and Raven.
Ra v0.2.1
Raven v0.0.3
I have a diploid genome for which other assemblers would juxtapose the two haplotypes instead of "crushing" them. I tested Ra and was …
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Full details in: https://github.com/SynBioDex/SEPs/blob/master/sep_025.md
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Hi,
We have several deeply sequenced bacterial genomes, pacbio reads with coverage up to 500x. Would it be possible to clarify whether such high coverage be an issue? Or is it beneficial to run wit…
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Hi
Im trying to use recycler for identifying circular elements from a mobilome (extracted plasmids from an environmental sample)
when i run the command: recycle.py -g ../assembly_graph.fastg -…
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The `final_plasmid.tsv` output file doesn't include a header. This makes it difficult to understand what each field represents.
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Proposal for a bridging path to merging ComponentDefinitions and ModuleDefinitions before SBOL 3 by the simple expedient of adding Interactions and Models to ComponentDefinition (and related changes).…
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Hello,
Steps:
1. installed kaiju
2. downloaded plasmid db from: http://kaiju.binf.ku.dk/database/kaiju_db_plasmids_2019-02-05.tgz
3. created ref db and index
4. ran kaiju for input files usin…