Badread v0.4.1

This release adds new error and qscore models called pacbio2021 that were trained on PacBio HiFi reads. Thanks to @kokyriakidis for pointing me to the datasets! Nothing else about Badread has changed, so no need to update unless you're interested in the new models.

Badread v0.4.0

This release adds a new way to define read identities: via a normal distribution of qscores. I added this because the original method (beta distribution) was awkward for high identities, e.g. PacBio HiFi reads. Both the old (identity beta) and new (qscore normal) methods are now available in Badread. See the Read identities section of the README for more details.

Badread v0.3.0

This version adds new Nanopore error/qscore models. These are named nanopore2023 and are now the default.

I also increased the default read accuracy from --identity 87.5,97.5,5 to --identity 95,99,2.5. This is slightly worse than I'd expect from real-world ONT R10.4.1 reads. I.e. using Badread v0.3.0's defaults should give you reads that are a bit worse than ONT R10.4.1 reads in 2023.

Badread v0.2.0

I made this version to include new Nanopore error/qscore models. These are named nanopore2020 and are now the default. For consistency, I renamed the old models from nanopore and pacbio to nanopore2018 and pacbio2016.

I also increased the default read accuracy by a bit from --identity 85,95,5 to --identity 87.5,97.5,5. This is to account for the fact that long reads are more accurate today than they were a few years ago. I still wanted Badread's defaults to be worse than real reads, but not too much worse 😄

Badread v0.1.5

This version changes some of the logic to ensure more accurate relative depths between reference contigs, even when those contigs are small and/or linear.

Badread v0.1.4

This release corresponds to the completion of Badread's review for JOSS. It has no code changes since v0.1.3 - just a few additions to the documentation.

Badread v0.1.3

• A little bit of refactoring
• Edits to README and comparison page
• Add a paper for JOSS

Badread v0.1.2

• More automated tests
• Bug fix: don't output 0-length reads
• Bug fix: don't crash when glitch values are between 0 and 1.

Badread v0.1.1

• Some small improvements to the stderr log
• New adapter option: give a number for the adapter sequence and Badread will make random adapters of that length

Badread v0.1.0

The first release of Badread!