Feature request - long read assembly graphs about graphbin

[Niicii]

+1 for Flye and maybe Miniasm as well

[Vini2]

Hi @susheelbhanu and @Niicii,

We have updated the GraphBin functionality so that GraphBin can work with Flye and Canu assemblies. Kindly note that since the assembly graph of Flye consists of edges (not the final contigs) we have used the assembly graph with edges and the corresponding edge sequences. We have also added a support script flye_miniasm_gfa2fasta.py to extract the edge sequences from the assembly graph file. Moreover, we are working on Miniasm functionality as well.

As @anuradhawick has mentioned, kindly note that we have developed GraphBin for Illumina short reads and the long-read assemblies might have sparsely connected graphs. This can make the label propagation less effective and may not result in improvements.

Thank you for your interest in our tool!

[susheelbhanu]

@anuradhawick: I was thinking of flye and canu. Thank you for helping with this!

[susheelbhanu]

Thanks a lot @Vini2. I'll give this a try and let you know if I run into any issues.

Best regards!!

[anuradhawick]

Hi @susheelbhanu

Assemblers have different formats for the graph. Could you be specific with the type of assembler(s) that you plan to use with GraphBin?

Kindly note that we have developed the tool for Illumina short reads and the long reads assemblies might have sparsely connected graphs. This can make the label propagation less effective. Let us know the assembler then we are happy to help how to proceed.

Thanks

[Vini2]

Hi @Niicii,

We have updated the GraphBin functionality so that GraphBin can work with Miniasm assemblies. Kindly note that since the assembly graph of Miniasm consists of unitig sequences we have used the assembly graph with unitig sequences. We have also added a support script flye_miniasm_gfa2fasta.py to extract the unitig sequences from the Miniasm assembly graph file.

Thank you for your interest in our tool!