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IRMA fails with too many reads

Status: Open.

#200 In theiagen/public_health_viral_genomics;

· frankambrosio3 opened on Dec 27, 2022

Implement workflow logic to use "mpox" as the target organism for TheiaCoV MPXV analysis

Status: Open.

#192 In theiagen/public_health_viral_genomics;

· frankambrosio3 opened on Nov 29, 2022

link to the notion page in 2.2.0

Status: Open.

#188 In theiagen/public_health_viral_genomics;

· neranjan007 opened on Nov 9, 2022

fastq-scan fails on large FASTQs

Status: Open.

#183 In theiagen/public_health_viral_genomics;

· kapsakcj opened on Oct 20, 2022

Floating NextClade SC2 lineage calls to output table

priority:3 (medium)

Status: Open.

#176 In theiagen/public_health_viral_genomics;

· kevinlibuit opened on Oct 3, 2022

TheiaCoV_Illumina_* if MPXV reference is not found, will use SC2 rather than error

Status: Open.

#168 In theiagen/public_health_viral_genomics;

· michellescribner opened on Aug 9, 2022

iVar amino acid data not outputted

Status: Open.

#167 In theiagen/public_health_viral_genomics;

· michellescribner opened on Aug 9, 2022

Gisaid assembly files produced for empty consensus fastas

Status: Open.

#153 In theiagen/public_health_viral_genomics;

· michellescribner opened on Jun 16, 2022

consensus_qc task not compatible with lowercase seqs in FASTAs

Status: Open.

#149 In theiagen/public_health_viral_genomics;

· kapsakcj opened on May 13, 2022

Issue with Medaka SC2 frameshifts and GISAID/GenBank rejections

Status: Open.

#136 In theiagen/public_health_viral_genomics;

· kevinlibuit opened on Apr 10, 2022

Adding TheiaCoV_FASTA and Augur workflows

Status: Open.

#135 In theiagen/public_health_viral_genomics;

· kevinlibuit opened on Apr 10, 2022

Adding sc2rf task to TheiaCoV workflows

Status: Open.

#123 In theiagen/public_health_viral_genomics;

· kevinlibuit opened on Mar 29, 2022