Spades Assembler output
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5.4 years ago
midox ▴ 260

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

Assembly spades contig • 3.8k views
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you should really have a contigs.fasta(g) and scaffolds.fasta(g) in your output. The final_ are usually in the K(kmer) folders.

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5.4 years ago
h.mon 32k

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

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5.4 years ago
MathGon ▴ 10

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

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