diamond
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bbuchfink
Accelerated BLAST compatible local sequence aligner.
This is probably a dumb question, but I don't understand why when I switch output format from 6 (blast-style) to 102 (taxonomy), the number of pairwise alignments changes. I made...
Hi, I used Diamond before by downloading all bacteria and archaea nonredundant protein sequences from RefSeq for makedb, but now with current version, I found that there is no taxonomy...
Hi, I was previously using Diamond and did not have any problem when I updated the database. However this time I kept getting this error ``` DIAMOND/2.0.8 is loaded diamond...
Hello, I built Diamond database using; `diamond makedb --in nr.gz \ –db nr_diamond –taxonmap prot.accession2taxid.FULL –taxonnodes nodes.dmp –taxonnames names.dmp –threads 72` and run diamond blastp to get a tabular file...
Hello, I am running diamond with these parameters: ``` for seq in `cat list_t.txt` do echo $seq diamond blastx -d $DIAMOND_NR -q 'fastq-join/'$seq'_merged.fastq' -o $seq'.daa' -f 100 done ``` and...
Hi, I am running `diamond blastx` on some individual eukaryotic scaffolds on a HPC environment with `slurm` with the following settings: ``` diamond blastx \ --query ${assembly} \ --db uniprot/reference_proteomes.dmnd...
Hi Benjamin, thanks a lot for developing and maintaining diamond. By monitoring tons of Diamond runs from Bakta (2k=80% query/subject coverage, --fast), I saw that a significant proportion of the...
Hi, Just in case this is of help, I was running diamond of DNA against a database of proteins, using: ``` --ultra-sensitive --iterate -e 0.001 --matrix BLOSUM45 --query-gencode 11 --top...
Code to reproduce (tried with v2.0.6 and v2.0.14): ``` echo -e ">test_gene\nMAAADGDDSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA" > test.fasta diamond makedb --in test.fasta --db test.dmnd diamond blastp -q test.fasta -d test.dmnd ``` Output of blastp...
Hello, I am trying to perform an all-vs-all BLASTP between a set (4716 in total) of predicted proteins. I ran the following command to generate the database: ``` diamond makedb...
