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can HMM_Flagger evaluate the quality of a haploid genome assembly?

Status: Open.

#65 In mobinasri/flagger;

· xingwu2 opened on Mar 19, 2026

Make flagger more lenient on lower coverage assemblies?

Status: Open.

#64 In mobinasri/flagger;

· cgroza opened on Jan 25, 2026

Could flagger be run on no Docker model?

Status: Open.

#62 In mobinasri/flagger;

· zhaochen-13 opened on Nov 26, 2025

Error: Floating point exception (core dumped)

Status: Open.

#60 In mobinasri/flagger;

· Enorya opened on Jun 23, 2025

Unable to create a properly formatted BAM file

Status: Open.

#58 In mobinasri/flagger;

· grbot opened on May 13, 2025

An example of using --runBiasDetection?

Status: Open.

#57 In mobinasri/flagger;

· vegetableyu opened on Apr 25, 2025

How to use Singularity to run hmm_flagger_end_to_end_with_mapping.wdl.

Status: Open.

#56 In mobinasri/flagger;

· vegetableyu opened on Apr 15, 2025

depth2cov is not available

Status: Open.

#52 In mobinasri/flagger;

· Golden-proteogenomics opened on Feb 12, 2025

Using flagger for de novo primary assemblies of diploid species

Status: Open.

#51 In mobinasri/flagger;

· DustinSokolowski opened on Feb 5, 2025

Segmentation fault with HMM-Flagger v1.1.0

Status: Open.

#50 In mobinasri/flagger;

· tbenavi1 opened on Feb 4, 2025

There is no final output

Status: Open.

#49 In mobinasri/flagger;

· wjq1981 opened on Jan 16, 2025

Segmentation fault with centromere annotation for bias detection

Status: Open.

#44 In mobinasri/flagger;

· baozg opened on Nov 5, 2024