From eb3bd558a63da76201f244b2c66d17d0b0714055 Mon Sep 17 00:00:00 2001 From: Olle Nordesjo Date: Tue, 30 May 2023 14:34:55 +0000 Subject: [PATCH] Update README.md, CHANGELOG.md, duplex_tools/__init__.py --- CHANGELOG.md | 4 ++++ README.md | 6 +++++- duplex_tools/__init__.py | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a162edf..445d316 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [v0.3.3] +### Added +- Deprecation warning. Update sam->bam in readme. + ## [v0.3.2] ### Added - Update to `dorado_stereo.sh`, do not create directories when using -n flag (dry run). diff --git a/README.md b/README.md index 9a7aff2..f5c0429 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ ![Oxford Nanopore Technologies logo](https://github.com/nanoporetech/medaka/raw/master/images/ONT_logo_590x106.png) +> **Deprecation notice** +> Please note that the functionality in this repository is superseded by integrated pairing in [Dorado](https://github.com/nanoporetech/dorado/tree/master/dorado). +> This means it's no longer necessary to use pairing or dorado_stereo.sh in order to perform end-to-end duplex calling. + # Duplex Tools Duplex Tools contains a set of utilities for dealing with Duplex sequencing @@ -58,7 +62,7 @@ For greatest duplex recovery, follow these steps: This will create an (unmapped) .sam file which has a mapping between the signal and bases. `--emit-moves` allows for additional pairs to be found in step 2b. - $ dorado basecaller dna_r10.4.1_e8.2_400bps_fast@v4.0.0 pod5s/ --emit-moves > unmapped_reads_with_moves.sam + $ dorado basecaller dna_r10.4.1_e8.2_400bps_fast@v4.0.0 pod5s/ --emit-moves > unmapped_reads_with_moves.bam ### 2a) Find duplex pairs for Dorado stereo/basespace basecalling This will detect the majority of pairs and put them in the `pairs_from_bam` directory. diff --git a/duplex_tools/__init__.py b/duplex_tools/__init__.py index f78513f..e3342e8 100644 --- a/duplex_tools/__init__.py +++ b/duplex_tools/__init__.py @@ -10,7 +10,7 @@ "split_on_adapter", "assess_split_on_adapter", "pairs_from_summary", "filter_pairs", "pair", "split_pairs"] -__version__ = '0.3.2' +__version__ = '0.3.3' def main():