Comments (7)
Thanks for your suggestion. We will consider adding this feature.
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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.
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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.
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Related Issues (20)
- Can vsearch combine two clustered-otutab together? HOT 4
- segmentation fault when printing out alignments HOT 2
- warnings with recent GCC (possible false-positives) HOT 1
- vsearch in R markdown issue HOT 5
- Sintax sometimes only outputs the ID with no further columns HOT 6
- fastq_mergepairs Fatal error: More reverse reads than forward reads HOT 6
- vsearch - usearch_global - maxhits only returns one hit HOT 3
- After combine two datasets together to recluster, some of the abundance of high-abundant OTUs were reduced dramatically. HOT 2
- vsearch tool detailed option in command line ? HOT 4
- Include rows of OTUs with no mapped reads in OTU tables
- EE: document the meaning of expected error values HOT 2
- appending sample names to fasta headers incomplete HOT 1
- Windows binaries: working with compressed files HOT 3
- --sizein seems having no effect in vsearch --usearch_global HOT 9
- Why FASTQ quality value above qmax is treated as Fatal error? HOT 5
- maxseqlength is not supported by makeudb_search command HOT 4
- Option to output the reason why merging failed
- Build errors with GCC 13 on Debian 13 HOT 8
- Too many "alignment score too low, or score drop too high" during pair-end merge compared with FLASH HOT 5
- fastq_mergepairs: merging stats should be written to log file if --log is used HOT 2
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