diamond

• 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.

• Fixed compiler errors on some systems.

• 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.

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

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

• 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.

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

• Highly improved performance of frameshift alignment mode.

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.

• Fixed query positions in pairwise format for translated searches.
• Changed default behaviour of --max-hsps option to report an unlimited number of HSPs for a single query/subject pair. Previously, only the single best HSP for a query/subject pair was reported. Since several HSPs are not uncommon for multidomain proteins and may contain valuable information, the default behaviour has been changed to report any HSP if its query and subject ranges are not enveloped by a higher scoring HSP.

• Fixed dbinfo command to be able to read older database formats.
• Adjusted XML format for better compatibility with Blast2Go.
• Fixed a potential error when running multiple instances of Diamond.

• Added option --xml-blord-format for alternative-style XML format.
• Fixed a bug that could cause a crash when writing compressed output files.

• Added --strand option to choose query strand for translated searches.
• Added dbinfo command to show information about a database file.

• Added taxonomic classification format.
• Fixed a bug in getseq printing masked residues.
• Fixed parsing of UniRef100_ sequence id prefixes.
• Added support for using the staxids output field in diamond view.

The taxonomic classification format is a new output format that does not print alignments, but only a taxonomic classification for each read using the LCA algorithm.

• Fixed a compiler error.

• Fixed compiler errors.
• Changed XML format for better compatibility with Blast2Go.

• Fixed compiler errors.

• Added support for named pipes.
• Added support for reading input files from stdin.
• Added more elaborate file I/O error messages.

• Improved performance.
• Fixed a bug in the query-indexed algorithm.
• Empty sequences are ignored instead of generating an error.

• Fixed a bug that could cause hanging.
• Fixed a bug that could cause an error when using the staxids output field and the --unal option.