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The version 3.2.0 update says that the "possibility to store only k-mers in the database (no counters)" was implemented; however, I don't see any documentation on how to do this. I m building some ve…
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Hello all,
In software docs, the 5 columns of output result file is a space-delimited list indicating the LCA mapping of each k-mer in the sequence(s). For example, "562:13 561:4 A:31 0:1 562:3" wo…
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**Submitting author:** @pierrepeterlongo (Pierre Peterlongo)
**Repository:** https://github.com/pierrepeterlongo/back_to_sequences/
**Branch with paper.md** (empty if default branch):
**Version:** v0…
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Hi,
We try to list all possible kmers from a pair of fastq files using:
```
kmc \
-k31 -m128 -ci1 -cs4294967295 -cx1e13 -t36 \
-jOutput.json \
@files.lst \
test.kmer.output \
`pwd`/kmc…
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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 I have been using a m…
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Hi,
I have met with another ignoring error, here is the log:
0.982908 k-mers per position
14994 DB matches per sequence
8 overflows
0 queries produce too many hits (truncated result)
58 sequen…
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Hi! Thanks for the great tool! I was wondering if one could get the genomic location of subgenome-specific TE or TE k-mer. My idea is to take a look at coding regions that are upstream and downstream …
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Why not allow gapped k-mers exists to search the best LCA?
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For canonical k mers, which ATCG combination is dropped?
For example, AAA, TTT, the kmc will dump all TTT counting to AAA or vice versa?
What's the rule? Thanks!
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I using the latest kmc code but i can't count kmer on fastq file. It work on fasta
```
$cat r1_test.fq
@0|Chromosome|4051100|4051286/2 BX:Z:CGACACGGTTTGGGCC
AAACCCAACCAC
+
FFFFFFFFFFFF
$kmc …