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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 the "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).