Compacted de-bruijn graph

Question

[sharmatina189059]

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.

[Rob]

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.

[sharmatina189059]

Can you please explain it little bit.

Answer 1

[lakhujanivijay]

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