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bingmann
COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
Hello COBS team, Any possibilities to also support amino acid sequences (20 alphabets instead of 4 for DNA). I found this to be extremely useful for genome query/search. Thanks, Jianshu
Hi, I am in charge to find presence of specific genes in 600.000 Salmonella's genomes. I used COBS on few genomes for training But I don't really understand the output......
…ndices Previously when combining multiple classic indices into a single classic index, the contents of source indices are read in as `char`. During the interleaving process, depending on the current...
When combining classic indices, for each batch the combinations of rows from each constituent index are written to an output block. The output block is reused for next batch. As...
Hi, COBS is slightly inconvenient for me to use because it does not recognize the .fna file extension for fasta files. I suggest supporting all common fasta file extensions. For...
Hi Timo, Would it be possible to get a conda package for cobs? I am having trouble compiling on my Mac and being able to access cobs through conda would...
I spent two hours finguring out how to compile cobs on our server (CentOS 7.9 with gcc 4.8.5) using conda. May this helps. 1. Create conda env and install new...
Would it be possible to increase the query length limit? I am wanting to query sequences up to 300kb and it would be good to avoid having to split the...
Could the number of k-mers in the query be included in the output so the user can calculate the percentage of the query in each dataset (or provide the percentage...