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Future: Enable gzipped unmapped fastq after 1st stage alignment

enhancement

Status: Open.

#413 In barricklab/breseq;

· jeffreybarrick opened on Jun 12, 2026

BreSeq as nf-core modules

Status: Open.

#407 In barricklab/breseq;

· zhliUU opened on Jan 14, 2026

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

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

merge info from different samples for downstream processing

feature-request

Status: Open.

#238 In barricklab/breseq;

· wmoebius opened on Apr 16, 2020

Compare across samples to improve predictions of low-frequency variants

coding-project

Status: Open.

#221 In barricklab/breseq;

· jeffreybarrick opened on Oct 11, 2019