Recommendation on k-mer counting package for multiple libraries?
1
0
Entering edit mode
4.0 years ago
johnnytam100 ▴ 100

I want to count all the 30-mers (or partially e.g. every 30-mer starting with "A") in multiple libraries to produce a k-mer abundance table partly like this :

kmer lib1 lib2 lib3 lib4 lib5
AAAAAAAAAAAAAAAAAAAAAAAAAGAGAA 0 0 2 6 4
AAAAAAAAAAAAAAAAAAAAAAAAAGATCT 0 1 1 0 2
AAAAAAAAAAAAAAAAAAAAAAAAAGGAAA 0 1 1 5 0
AAAAAAAAAAAAAAAAAAAAAAAAAGGAAG 1 0 0 0 5
AAAAAAAAAAAAAAAAAAAAAAAAAGGAGG 0 0 1 0 1

Any recommendation on what package to use on a linux system?

Thank you!

kmer • 858 views
ADD COMMENT
2
Entering edit mode
4.0 years ago
5heikki 10.0k

I use Jellyfish 2 for k-mer counting.

ADD COMMENT

Login before adding your answer.

Traffic: 2241 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6