Compacted de-bruijn graph
1
0
Entering edit mode
4.1 years ago

Hello all I am interested in developing and analysing compacted de-bruijn graph for a number of same genes from different strains. this link (https://github.com/Malfoy/bcalm) provides a algorithm for compacted de-bruijn graph.But I am unable to understand the input of this algorithm. Can anybody tell me other tools for same purpose. Please elaborate as I am new to this.

assembly • 908 views
ADD COMMENT
0
Entering edit mode

You may also consider using Bcalm2 (https://github.com/GATB/bcalm) instead of the original Bcalm. It is more actively developed / maintained, and performs better as well.

ADD REPLY
0
Entering edit mode

Can you please explain it little bit.

ADD REPLY
0
Entering edit mode
4.1 years ago

Isn't that loud and clear at that link

Each line in the input file is a distinct k-mer in upper-case, ending with his counting (not required). Here is a sample input:

AATCGATCG 3 ATCGATCGT 33 TCGATCGTA 645
ADD COMMENT

Login before adding your answer.

Traffic: 1928 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