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Roadmap: releases after v1.0.0
#90 · MaximilianStammnitz opened on Oct 22, 2026

Barcoded DMS: long-read barcode–variant association and short-read barcode counting
Enhancement
nf-core/deepmutscan#91 · opened on Oct 23, 2026 · v2.x: beyond one ORF and saturation mutagenesis libraries
Roadmap: releases after v1.0.0
nf-core/deepmutscan#90 · opened on Oct 22, 2026
Multi-codon variant libraries (designed higher-order mutants)
Enhancement
nf-core/deepmutscan#89 · opened on Oct 22, 2026 · v2.x: beyond one ORF and saturation mutagenesis libraries
In-frame insertion and deletion (indel) variants
Enhancement
nf-core/deepmutscan#88 · opened on Oct 22, 2026 · v2.x: beyond one ORF and saturation mutagenesis libraries
Optional re-pairing of out-of-order mates (--repair_pairs)
Enhancement
nf-core/deepmutscan#86 · opened on Oct 22, 2026 · v1.1.0: robustness
Multi-ORF support
Enhancement
nf-core/deepmutscan#83 · opened on Oct 18, 2026 · v2.x: beyond one ORF and saturation mutagenesis libraries
Single-end read mode
Enhancement
nf-core/deepmutscan#81 · opened on Oct 18, 2026 · v1.4.0: read input diversification
Read adapter (or base quality-dependent) pre-trimming
Enhancement
nf-core/deepmutscan#80 · opened on Oct 8, 2026 · v1.4.0: read input diversification
Interactive 3D protein structure viewer – config enhancement
Enhancement
nf-core/deepmutscan#79 · opened on Oct 8, 2026 · v1.1.0: robustness
SNV error rate improvements & mutational signature support
Enhancement
nf-core/deepmutscan#72 · opened on Oct 5, 2026 · v1.2.0: sort-seq and improved count error model
Enrich2 and rosace support
Enhancement
nf-core/deepmutscan#71 · opened on Oct 5, 2026 · v1.3.0: more fitness estimators
Overall efficiency tuning of the pipeline
Enhancement
nf-core/deepmutscan#70 · opened on Oct 5, 2026 · v1.4.0: read input diversification
Support for FACS / sort-seq data
Enhancement
nf-core/deepmutscan#67 · opened on Oct 5, 2026 · v1.2.0: sort-seq and improved count error model

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Barcoded DMS: long-read barcode–variant association and short-read barcode counting

Roadmap: releases after v1.0.0

Multi-codon variant libraries (designed higher-order mutants)

In-frame insertion and deletion (indel) variants

Optional re-pairing of out-of-order mates (`--repair_pairs`)

Multi-ORF support

Single-end read mode

Read adapter (or base quality-dependent) pre-trimming

Interactive 3D protein structure viewer – config enhancement

SNV error rate improvements & mutational signature support

Enrich2 and rosace support

Overall efficiency tuning of the pipeline

Support for FACS / sort-seq data