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samtools markduplicate usage

Status: Open.

Bug

#200 In sanger-tol/readmapping;

· muffato opened on Jan 21, 2026

Extra <code>--output-fmt cram</code>

Status: Open.

Bug

#198 In sanger-tol/readmapping;

· muffato opened on Jan 20, 2026

Warnings in the HiC minimap2_align module

Status: Open.

Bug

#197 In sanger-tol/readmapping;

· muffato opened on Jan 20, 2026

Select short aligner based on genome size

enhancementImprovement of the existing featuresImprovement of the existing features

Status: Open.

Task

#194 In sanger-tol/readmapping;

· sainsachiko opened on Jan 15, 2026

Standardize the filtering and processing options

enhancementImprovement of the existing featuresImprovement of the existing features

Status: Open.

Feature

#189 In sanger-tol/readmapping;

· muffato opened on Nov 28, 2025

Implement sanger-tol cramalign for Illumina and long read data

enhancementImprovement of the existing featuresImprovement of the existing features

Status: Open.

Task

#187 In sanger-tol/readmapping;

· sainsachiko opened on Oct 3, 2025

Standardize file naming convention

enhancementImprovement of the existing featuresImprovement of the existing features

questionFurther information is requestedFurther information is requested

Status: Open.

Task

#182 In sanger-tol/readmapping;

· sainsachiko opened on Aug 22, 2025

Include FastK k-mer histogram files/db for GenomeScope and related tools

enhancementImprovement of the existing featuresImprovement of the existing features

good first issueGood for newcomersGood for newcomers

Status: Open.

Feature

#167 In sanger-tol/readmapping;

· sainsachiko opened on Jun 3, 2025

Generate Hi-C insert length distribution plots from BAM/CRAM

Status: Open.

Feature

#166 In sanger-tol/readmapping;

· sainsachiko opened on Jun 3, 2025

Generate samtools stats with Standard Flags (_F0x900.stats, _F0xB00.stats) for Illumina Data QC

enhancementImprovement of the existing featuresImprovement of the existing features

featureRequests for new featuresRequests for new features

Status: Open.

Feature

#165 In sanger-tol/readmapping;

· sainsachiko opened on Jun 3, 2025

Investigate impacts of read filtering on PacBio data

enhancementImprovement of the existing featuresImprovement of the existing features

questionFurther information is requestedFurther information is requested

Status: Open.

Feature

#163 In sanger-tol/readmapping;

· sainsachiko opened on Jun 3, 2025

Methylation calls

enhancementImprovement of the existing featuresImprovement of the existing features

questionFurther information is requestedFurther information is requested

user requestRequests made by users and publicRequests made by users and public

Status: Open.

Feature

#159 In sanger-tol/readmapping;

· muffato opened on May 16, 2025