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Published by bbuchfink over 6 years ago
full_sseq
to tabular output format.Published by bbuchfink over 6 years ago
Published by bbuchfink over 6 years ago
Published by bbuchfink over 6 years ago
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
Published by bbuchfink over 6 years ago
Published by bbuchfink over 6 years ago
--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.-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.--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.--range-cover
. Note that this feature is currently only available in frameshift alignment mode.Published by bbuchfink over 6 years ago
Published by bbuchfink over 6 years ago
Published by bbuchfink almost 7 years ago
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.
Published by bbuchfink almost 7 years ago
--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.Published by bbuchfink almost 7 years ago
Published by bbuchfink almost 7 years ago
--xml-blord-format
for alternative-style XML format.Published by bbuchfink about 7 years ago
--strand
option to choose query strand for translated searches.dbinfo
command to show information about a database file.Published by bbuchfink over 7 years ago
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.
Published by bbuchfink over 7 years ago
Published by bbuchfink over 7 years ago
Published by bbuchfink over 7 years ago
Published by bbuchfink over 7 years ago
Published by bbuchfink over 7 years ago
Published by bbuchfink over 7 years ago