Alignment to fastg assembly graph

Question

[grp2009]

Briefly, I am trying to automate the process of aligning a query sequence (from FASTA) to an assembly graph (FASTG from Spades assembly). As output I need the sequences of the paths in the assembly graph corresponding to the alignment(s).

More detail: I have used Spades to assemble the genome from a diploid yeast starting with short reads (WGS sequencing). Using the wonderful program Bandage I am then able to BLAST a certain query sequence against the assembly graph (FASTG file). Because of the diploid nature of the genome, the result looks like this:

There are two paths corresponding to this BLAST alignment. In Bandage I can select the nodes corresponding to a path, and then export that path's sequence to a FASTA file.

Doing this manually gives me exactly what I want (essentially, haplotypes derived from the assembled genome). However, I would very much like to automate this process. What tools should I be looking into?

Answer 1

[grp2009]

I didn't realize it when I posted the question, but Bandage has a command line mode, including a command querypaths that accomplishes precisely the task in question.

First, find out where the Bandage executable lives. On a Mac, you select the Bandage application, do "Show Package Contents", and the executable is in Contents/MacOS/Bandage. I will just call this executable Bandage.

Then you can run

Bandage assembly_graph.fastq query_sequence.fasta output_prefix

and it will produce output_prefix.tsv with the exactly the paths desired! What a wonderful program. Note that it works with both fastg and gfa formats as input.

[GenoMax]

Thank you for providing an answer/closure for the question. It will help someone in future.