kmer-db

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limitations ?

1

--Hi, program failed with a list of 200000 entries kmer-db build -k 21 -multisample-fasta input.list DGV-kmer-21.db Kmer-db version 1.10.0 (18.07.2022) S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A....

lmanchon

Much fewer k-mer loaded from database during new2all

2

Hi, I was running kmer-db with a relative large database, but I encountered a problem that greatly reduced the number of shared k-mers. **The database was constructed from all bacteria...

nekokoe

Dear authors: I got some of my interest kmers with counts and want to calculate there relationship by kmer-db. But it seems noway to input kmer-table to kmer-db. Please give...

biozhangzhou

one2all/new2all output counts for common k-mers between multiple db-samples

3

Hi! The one2all/new2all give this information about the intersection sizes with a new sample: s1: 100/150 s2: 200/300 s3: 50/1000 ... Is there any way to get more detailed information...

mihkelvaher

Seed for minhash algorithm

8

I've read the paper for kmer-db and I weren't able to find anywhere whether kmer-db uses a seed for minhashing during the build step. I've ran kmer-db build twice (from...

CBorreda

option to include non-canonical k-mers

1

Hi, I was wondering if it is possible to include an argument in kmer-db that allows the inclusion of non-canonical k-mers in the construction and querying of databases. Thus far...

haneubau

build step failed after throwing an instance of 'std::bad_alloc'

1

I am trying to build a kmer db using the k-mer output from KMC but I keep getting an error. This is the command I am running: ``` ./kmer-db build...

rmormando

short read data

1

I have Illumina short-read sequences I want to use as an input will the tool take that into account when creating a database? The samples are labeled as`Sample1_R1.fasta Sample1_R2.fasta` would...

rmormando

Illegal instruction while running kmer-db

1

Hi there, I am actually running kmer-db as a part of SqueezeMeta's dependencies, but even when I do a fresh install via conda in a new environment (versions 1.11.1, 1.7.6,...

gracegyho

Enhancement Request: Including Specific kmer Information in Output Files

1

I really appreciate the advantages of your tool kmer-db compared to other tools, and I'm very interested in using it. However, I noticed that the result files (all2all, new2all, and...

qbdong122