Comments (7)
Thanks for your suggestion. We will consider adding this feature.
from vsearch.
The new allpairs_global option is now implemented. It performs optimal global alignment of all pairs of sequences in the specified file. It uses no heuristics and is multi-threaded. It reports all alignments when the --acceptall option is specified, otherwise use the --id option and other accept/reject options.
from vsearch.
Many thanks!
from vsearch.
I hope it works as it should. As it performs an optimal alignment for all pairs of sequences it may be slower than usearch in some cases, but in return you are guaranteed the optimal alignment for all. Also, it's multi-threaded. Please report any problems you may encounter.
from vsearch.
I've tested all options. Everything works correctly, except the --acceptall
option:
vsearch --allpairs_global tmp.fas --acceptall --userout tmp.userout
vsearch v1.0.4_linux_x86_64, 15.6GB RAM, 4 cores
Fatal error: Specify either --acceptall or --id with an identity from 0.0 to 1.0
I've tried all possible combination of --acceptall
and output options, none of them works.
I was also wondering if the --sizein
option should be accepted too? It would shorten the sequence identifiers in output files.
from vsearch.
Sorry for that bug. Resolved in 1.0.5.
from vsearch.
How should the --sizein option work in this case. I do not understand.
from vsearch.
Related Issues (20)
- maxseqlength is not supported by uchime_denovo command HOT 6
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- Issue related to usearch_global match HOT 4
- missing userfields options
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- Obtaining the expected error for each read HOT 4
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- Can't run static binary HOT 3
- is there a major vote fraction parameter of a vsearch clustered consensus sequence? HOT 5
- usearch_global command eats my sample IDs HOT 3
- USEARCH wants to go open-source? HOT 3
- Adapt for RISC-V HOT 2
- centroid sequence length after clustering is different from input sequences' length which are all equal to 200n HOT 2
- unexpected behaviour - v 2.28 sintax chooses first sequence when not classifiable HOT 4
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