DIAMOND v0.9.23

• Added shortcut --long-reads to set suitable parameters for long read alignment: --range-culling (query range-based hit culling), --top 10 (locally report hits within 10% of the best alignment score) and -F 15 (use frameshift alignment mode).
• Fixed a performance issue for very long query sequences. The "longs reads" mode can now efficiently align query sequences that are several megabases in length.
• Added support for using a FASTA file instead of a Diamond database as the --db parameter in alignment workflows. Note that this incurs substantial overhead and should not be used for large databases.
• Fixed an issue that could cause too high memory usage.
• Added output field qqual to print query FASTQ quality values to the tabular format.
• Changed license to GPL.
• Raised compiler requirement to GCC 4.6.
• Added option to use the DAA output format for diamond view.
• Added CL (command line) and VN (version) fields to the @pg SAM format header line.

DIAMOND v0.9.22

• Added output field full_sseq to tabular output format.
• Database sequences that exceed the maximum accession length will no longer cause an error.
• Added support for PAF output format.
• Optimized performance of database taxonomy filtering.

DIAMOND v0.9.21

• Fixed compiler errors on some systems.

DIAMOND v0.9.20

• Added Bioconda installation instructions to the manual.
• Added official docker release: https://hub.docker.com/r/buchfink/diamond/
• Fixed a bug that could cause corrupted output if compression was activated.
• Fixed an issue that could cause high memory usage by automatic use of the query-indexed algorithm.

DIAMOND v0.9.19

This release provides the option to conduct filtered searches by taxonomy. Using --taxonlist followed by a comma-separated list of NCBI taxonomy IDs will search only against matching reference sequences. Any taxonomic rank can be used. For example, use --taxonlist 562 to search against all E. coli sequences; use --taxonlist 2 to search against all bacterial sequences.

This feature requires taxonomy data to be built directly into the database. The --taxonmap and --taxonnodes options now need to be provided exclusively to the makedb command if taxonomy features are to be used.

This release changes the database format and requires database rebuilding. To rebuild the database from an existing one, a Unix pipe can be used like this:
/path/to/old/diamond getseq -d dbfile | /path/to/new/diamond makedb -d newdb

DIAMOND v0.9.18

• Optimized output writing performance.
• Fixed a bug in the XML output format.

DIAMOND v0.9.17

• Added option --range-culling to restrict hit culling to overlapping query ranges. This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance.
  Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits.
  Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range.
  The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode.
• Fixed a compiler error on FreeBSD.
• Fixed escape sequences in XML output.

DIAMOND v0.9.16

• Fixed a bug that caused an error for non-SSSE3 builds.

DIAMOND v0.9.15

• Highly improved performance of frameshift alignment mode.

DIAMOND v0.9.14

Added support for frameshift alignments (option -F to set the frameshift penalty). For example: diamond blastx -F 15 ...

Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads.

In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1
nucleotide in the direction of translation respectively.

Note that this feature is disabled by default. This release changes the DAA format. DAA files created by this version are not backward compatible with previous versions.