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Replace shigapass with shigatyper in create-yaml

Status: Open.

#47 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Apr 21, 2026

Change the yaml file to updated manifest format

Status: Open.

#42 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Mar 31, 2026

Remove post-align-qc when bonsai-prp has a parser for samtools stats and samtools bedcov

Status: Open.

#39 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Mar 26, 2026

Conversion and inclusion of perl run assembly trim clean used for Ion Torrent

Status: Open.

#24 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Mar 16, 2026

Conversion and inclusion of perl masking script

Status: Open.

#21 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Mar 16, 2026

Add qc figure generation to tb validation notebook

Status: Open.

#9 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Oct 2, 2024

Fix generation of matrix

Status: Open.

#8 In SMD-Bioinformatics-Lund/jasentool;

· ryanjameskennedy opened on Sep 4, 2024

Sample id needs to be unique which is a combination of lims and seqrun

Status: Open.

#2 In SMD-Bioinformatics-Lund/jasentool;

· svartapaerlan opened on Jun 7, 2024