InSilicoSeq Versions Save

What's Changed

• Fixed the instructions to run with docker
• fix crash when using --coverage (#253)

New features and improvements

• amplicon simulation with --sequence_type amplicon (and optionally --readcount)
• new and updated error models (including NextSeq, and MiSeq models with different quality thresholds)
• improved memory usage and performance

Bug fixes

• iss now always simulates the correct number of reads
• fix incorrect insert size distributions in existing models

Other

• switch to pytest
• linting and formatting

• Now works with latest numpy and Biopython
• move tests to pytest
• fix #220

• Changes requirements to biopython <= 1.78

Bugfix release.

• Fix for #202

Bugfix release:

• Documentation clarification for --coverage_file (#191 )
• iss generate should now produce the correct amount of reads even for highly fragmented genomes (#195)

Bugfix release:

• Fix for #189 (thanks to @emollier )

The release fixes a few bugs and brings some improvements to existing options.

⚠️ This release also deprecates python <= 3.5 ⚠️

Improvements:

• the coverage option now accepts distributions (same than --abundance) and scales them accordingly to --n_reads(#127)
• the old --coverage option has been renamed --coverage_file
• --draft is now usable with abundance and coverage files (#83)

Bugfixes:

• the documentation should build properly again (#163)
• iss will not throw an error if invoked without options (#177)

Bugfixe release:

• iss generate does not crash on sequences shorter than template length anymore
• iss generate does not crash on model with no sequences with Q>20
• --ncbi does not abruptly crash when downloading large numbers of genomes anymore

Bugfix release:

• Fix for #133