SciLifeLab/umi-transfer: Version 1.5.0 - "Able adenine"

To increase the accuracy of quantitative DNA sequencing experiments, Unique Molecular Identifiers may be used. UMIs are short sequences used to uniquely tag each molecule in a sample library, enabling precise identification of read duplicates. They must be added during library preparation and prior to sequencing, therefore require appropriate arrangements with your sequencing provider.

Most tools capable of taking UMIs into consideration during an analysis workflow, expect the respective UMI sequence to be embedded into the read's ID. For some library preparation kits and sequencing adapters, the UMI sequence needs to be read together with the index from the antisense strand. Consequently, it will be output as a separate FastQ file during the demultiplexing process.

This tool efficiently integrates these separate UMIs into the headers and can also correct divergent read numbers back to the canonical 1 and 2.

New and Improved Features:

• Since this release, umi-transfer features internal multi-threaded output compression. As a result, umi-transfer 1.5 now runs approximately 25 times faster than version 1.0 when using internal compression and about twice as fast compared to using an external compression tool via a buffered pipe.
• The new CLI arguments -t, --threads <NUM_THREADS> and -l, --compression_level <COMPRESSION_LEVEL> have been introduced accordingly. The compression level defaults to 3. Higher numbers result in marginally smaller files but take significantly longer to compress. For the number of threads, we recommend 9 or 11, if a sufficient number of logical cores are available.
• The Docker base image has been updated from Debian Bullseye (Version 11) to Debian Bookworm (Version 12).
• Improved integration tests, including CLI prompts.
• Updates to the internal Rust libraries and dependencies.

Discontinued Previous Features:

• None

Changes in detail:

• Update the Rust CI on the main branch by @MatthiasZepper in https://github.com/SciLifeLab/umi-transfer/pull/12
• Implement multi-threaded FastQ compression for umi-transfer by @MatthiasZepper in https://github.com/SciLifeLab/umi-transfer/pull/11
• Polishing for 1.5 release by @MatthiasZepper in https://github.com/SciLifeLab/umi-transfer/pull/13
• Version 1.5.0 release PR - "Able adenine" by @MatthiasZepper in https://github.com/SciLifeLab/umi-transfer/pull/14

Full Changelog: https://github.com/SciLifeLab/umi-transfer/compare/v1.0.0...v1.5.0