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This will build on #13 which handles the query FASTA file fragmentation, subject file BLAST database building, and actually running NCBI BLAST to compare the fragmented query to the subject database.
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## Tasks
1. all PCGs BLAST all-vs-all search - diamond.py
2. gene sets construction
3. real alignments to respective sample contigs specific to gene coordinates
4. module detection of coverage-c…
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Dear NIQKI team,
I am using 60,000 reference genomes and 8,000 query genome like this:
nohup time niqki --index gtdb_r207.name.txt --query TaraOceanMAG.name.txt --kmer 16 --sketch 10 --pretty…
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here are some thoughts I wrote up for a collaborator, thought I'd share broadly -
The default FracMinHash approach will yield overlap estimates when applied to two metagenomes. In technical terms t…
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I feel like this type of method would work as a fantastic competitor to bacterial whole genome alignment software such as Mauv/progressiveMauve. Have you tried validating this software with bacterial …
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I have a question concerning the recommended workflow.
I used short reads to create the input VCF file and the ont long reads in whatshap.
I used the pipeline below but my haplotype a nearly the s…
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**EDIT I guess it would help if I were to read the publication to see especially the figures on time and amplitude domains' effects on base identity.**
Hi, thank you very much for developing this t…
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I am running the latest version of Grandeur and erroneously getting an error (maxcpus isn't a supported param), even though I am not using that param. Here is my command-line and the error message: …
DrB-S updated
1 month ago
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Main points:
* Expand https://github.com/pyani-plus/pyani-plus/blob/main/pyani_plus/private_cli.py with another function ``log_dnadiff`` (like the existing ``log_anim``, ``log_anib``, ``log_fastani…
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The running time of Linculst in the threshold between 50% to 90% is normally the same. But why does Linclust‘s running time in the threshold 90% to 100% range gradually increase? The run time at 100% …