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Paired-End breseq Analysis Fails to Detect PCR-Verified Gene Knockout at Full Coverage

Status: Open.

#404 In barricklab/breseq;

· khairnarsnehal940 opened on Oct 17, 2025

configure ignores <code>--with-static-zlib</code> (with analysis and temporary work-around)

Status: Open.

#402 In barricklab/breseq;

· jpgoldberg opened on Sep 7, 2025

Remove internal samtools/htslib compile

enhancement

Status: Open.

#399 In barricklab/breseq;

· jeffreybarrick opened on Jun 14, 2025

GDTools COMPARE TSV output headers can vary

Status: Open.

#395 In barricklab/breseq;

· jvera888 opened on May 9, 2025

Joint Junction Mutation and Repeat Expansion Interpretation

Status: Open.

#389 In barricklab/breseq;

· zahraa992 opened on Dec 19, 2024

In-frame indels shouldn't necessarily be "genes_inactivated"

Status: Open.

#385 In barricklab/breseq;

· dannagifford opened on Oct 11, 2024

How to judge some unassigned evidence in my experiment

Status: Open.

#383 In barricklab/breseq;

· Gia1120 opened on Oct 7, 2024

Identify linked mutations from mapped reads

feature-request

Status: Open.

#357 In barricklab/breseq;

· spleonard1 opened on Sep 8, 2023

compare tables should always display sample names used to generate them

enhancement

Priority-Low

Status: Open.

#283 In barricklab/breseq;

· danieldeatherage opened on Aug 19, 2021

Add a tutorial for how to predict genomic insertions of a cassette.

documentation

Status: Open.

#278 In barricklab/breseq;

· jeffreybarrick opened on Aug 13, 2021

Make JC evidence in HTML tables more readable

Status: Open.

#273 In barricklab/breseq;

· jeffreybarrick opened on Jul 22, 2021

Remove requirement for 'which' command

Status: Open.

#263 In barricklab/breseq;

· jeffreybarrick opened on May 28, 2021