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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Update medaka version #127

Closed laura-bankers closed 10 months ago

laura-bankers commented 10 months ago

Hello,

We are using Artic --medaka for assembly of SARS-CoV-2 tiled amplicon WGS. Given updates to guppy and ONT chemistry are there any plans to update the medaka version available with Artic in order to access the medaka models that account for these updates?

BioWilko commented 10 months ago

1.2.4 now uses medaka 1.8.0, the conda version should update soon after tests pass

laura-bankers commented 10 months ago

Thank you so much for the incredibly speedy reply/action, I really appreciate it!

Laura

On Tue, Aug 22, 2023 at 7:38 AM Sam W @.***> wrote:

Closed #127 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_artic-2Dnetwork_fieldbioinformatics_issues_127&d=DwMCaQ&c=sdnEM9SRGFuMt5z5w3AhsPNahmNicq64TgF1JwNR0cs&r=Kuwi0r_q2tQHiF3gSjmAavw2z7dViOrLkc3pycL1AA8&m=dhZKzXdeNngL-LF6D9KZWdKRlR1LUIu5V-3VcvASlxOfxoKCPv_seciNDRf9tvfg&s=e0188CKF3tIC4yNKyWY66Zaea12xOX9VTlKmr5FPwMQ&e= as completed.

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-- Laura Bankers, PhD Bioinformatics and Genomic Analysis Supervisor Colorado Department of Public Health and Environment @.*** (303) 692-3293