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Hi,
I would like to use the created index from:
http://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/
To run a query (Salmonella's sequences) with COBS
Could you tell me which folder I need to download (sorry I am very new in the field) ?

Thank you

Hello,

We built an index over RefSeq genomes. The downloaded filenames are named like this:

/path/GCF_000019125.1_ASM1912v1_genomic.fna.gz
/path/GCF_000019165.1_ASM1916v1_genomic.fna.gz
...

When searching the index, the result looks as follows:

*query1 XXX
GCF_000019125 XXX
GCF_000019165 XXX
...

Luckily for us, the names are still unique and we should be able to compare the output with some effort to reconstruct the full reference name.

This format is lossy if the names weren't unique before the first dot and might even lead to severe false negatives if not noticed by the user.

Best,
Svenja

Hi,
it seems queries are only supported when stored in fasta format.
Do you have any plan to enable query from reads in fastq.gz files?

Thanks,
-Giulio

Could the percentage/proportion of query kmers present in each sample be reported rather than the number of kmers present?

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...
I copied a subsequence (55 bp) from one of my genomes, and run COBS to see if it get it.
In the output I got 24 (see bellow).
And when I choose bigger sub sequence, sometimes it doesn't find it at all.

Another issue: how I can see if my query fully matchs or partially?

I ran these command:
cobs compact-construct index.cobs_compact
cobs query -i index.cobs_compact

--- end of document list (5 entries) ---
documents: 5
minimum 31-mers: 2811023
maximum 31-mers: 2874904
average 31-mers: 2834688
total 31-mers: 14173442
DIE: Output file exists, will not overwrite without --clobber @ /opt/conda/conda-bld/cobs_1646087618998/work/cobs/construction/compact_index.cpp:213
terminate called without an active exception

SRR18349609 24
SRR18349610 24
SRR18349611 24

TIMER info=search hashes=9.929e-06 io=0.000567883 total=0.000577812

Query length 55

I'd really appreciate your help

Thank you!

Right now COBS on Mac has to be compiled by users. We can't provide a conda recipe because COBS require gcc. We can't use containers as singularity is not supported on Mac. The real solution for this is for COBS to compile with clang, then it is straightforward to provide a COBS Mac bioconda recipe