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Spades assembler output

Hi!

Just I want to know what are the differences between the two outputs files, scaffolds.fasta and contigs.fasta in the assembler spades.py.

The manual don't provide any useful information at all. Please I don't want the definition of a conting or a scaffold, what I trying to understand is the technical part behind the spades algorithm, for example maybe spades.py is assuming that I am using any Illumina 1.9 sequencing machine but that's not enough information to determine the scaffolds or is it? How a scaffold is determined in the De Bruijn graph versus a conting? How spades.py knows the insert size of the specific protocol used to sequence, or just assumes one?

Help I am a little lost.

Any information will be useful.

Here is the manual's link http://spades.bioinf.spbau.ru/release3.6.2/manual.html#sec3.5

assembly
• 11,882 views • link
updated by Ram Ram • written by elbecerrasoto • elbecerrasoto

Because scaffolds and contigs are terms used by most assemblers. A scaffold is a construct of multiple contigs bridged by poly N characters. What it means is that a region between contigs cannot be resolved by the assembler despite knowing the orientation of 2 contigs relative to each other.

• 0 views • link
written by apelin20 apelin20

can you explain the contigs orientation?
have an example please.
Thanks

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written by midox midox

thanks.

how we know the distance between the two paired reads?

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updated by Ram Ram • written by midox midox

You can map your paired reads to a reference, like an assembled genome, and create a bam file. Then you can use CollectInsertSizeMetric from picard tools to estimate distance between two paired ends.

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written by apelin20 apelin20

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