Question: Spades Assembler output
0
gravatar for midox
5.0 years ago by
midox260
Tunisia
midox260 wrote:

hello,
I used Spades for assembling short reads.
in the Spades_output, i have two files "final_contigs.fasta" and "final_contigs.fastg".
what's the fastg format?
and what file should I take for my research?

thanks

spades contig assembly • 3.7k views
ADD COMMENTlink modified 5.0 years ago by MathGon10 • written 5.0 years ago by midox260
1

you should really have a contigs.fasta(g) and scaffolds.fasta(g) in your output. The final_ are usually in the K(kmer) folders.

ADD REPLYlink written 5.0 years ago by Adrian Pelin2.4k
1
gravatar for h.mon
5.0 years ago by
h.mon31k
Brazil
h.mon31k wrote:

If you read carefully the SPAdes manual, you will find a link to the FASTG format specification. Its first paragraph:

This document introduces a prototype format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. It is called FASTG, like FASTA, but the G stands for 'graph'.
ADD COMMENTlink written 5.0 years ago by h.mon31k

Yes that's true.
I have not seen.
thank you

ADD REPLYlink written 5.0 years ago by midox260
1
gravatar for MathGon
5.0 years ago by
MathGon10
France
MathGon10 wrote:

As mentioned, .fastg is a graph file. You can open it with Bandage to show lins between your contigs.

ADD COMMENTlink written 5.0 years ago by MathGon10
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