DIAMOND v2.0.10

[bbuchfink]

• Using BLAST databases now requires a preprocessing step using the command prepdb. The command line is: diamond prepdb -d /path/to/database. This call runs quickly and will write some small auxiliary files into the database directory.
• Improved performance of searching small query files.
• Added "iterative" search mode (option --iterate) to search the query dataset with increasing sensitivity, only searching queries at the target sensitivity that do not produce a significant alignment at a lower sensitivity search. For example, using --sensitive --iterate will first search the query file at default sensitivity, and search all query sequences again in --sensitive mode that fail to align in the first round.
• Added the "global ranking" mode (option -g) to set a limit on the number of Smith Waterman extensions per query, with the target sequences ranked by their ungapped extension scores.
• Added the --fast sensitivity mode that is faster and less sensitive than the default mode.
• Reduced the time for loading target sequences from BLAST databases.
• Added the contiguous-seed mode (option --algo ctg) to improve performance for small query files.
• Added support for using --comp-based-stats (3,4) in combination with --ext full.
• Fixed a bug that could cause a Traceback error when using --comp-based-stats (3,4) in rare cases.
• Changed the full_sseq output field to always contain unmasked sequences.
• Fixed an issue that could cause target output order to be nondeterministic in case of identically scoring hits.
• Added support for reading zstd-compressed input files (auto-detected) and writing zstd-compressed output files (option --compress zstd) (requires compilation using cmake -DWITH_ZSTD=ON).
• Compilation with BLAST database support requires the zstd library.
• Added error message when reading protein sequences from FASTA files that only contain DNA letters (can be disabled using --ignore-warnings).

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This discussion was created from the release DIAMOND v2.0.10.