Reference assisted whole-genome assembly pipeline - YEAST!

Question

[palu]

Hello All! iam new at BIOSTARS so I hope this is the right place to put my question.

My case: We have sequenced 3 yeast strains (not cerevisiae) and we would like to go through the whole genome assembly pipeline. We have different reference genomes available -> closed and draft genome references.

Here are the sequencing specifications: **Illumnia MiSeq

around 8,5 million reads each way (paired ends)

most reads around 90-120 bp long

high coverage: around 90x**

I would like to know what are recommanded tools for the diffrent steps in the pipeline, which takes into account our specifications. So far we thought about:

Assessing quality: FastQC, or...

trimming/ cut adaptors,primers: Cutadept or AdapterRomoval, or...

Initial contig building: Discovar or SOAPdenovo or Abyss or SPAdes 3.9, or...

Scaffolding: Medusa, or...

What tools would you suggest?

Thanks and best regards!

Answer 1

[Medhat]

For the first part (Assessing quality, trimming/ cut adaptors,primers) most tools will do the job BBMap will help you to achive all of this

The second part (contigs and scaffolding) you will need to try different tools and different configuration till you get the best result you can use QUAST.

also some reads before jumping to work will help

A comprehensive evaluation of assembly scaffolding tools

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

[zizigolu]

BBMap is really perfect

[dago]

Isn't QUAST comparing assembly and not performing the assembly and scaffolding itself?

[Medhat]

yes. I am saying after using different tools for assembly you can compare your result using QUAST

[dago]

Ok, now is clear. Thanks

Answer 2

[palu]

What exactly do you mean with first and second part?

Answer 3

[Lina F]

I am also trying to get started with yeast whole genome assembly. I have reference information as well (draft contigs) and was reading about SPAdes to generate contigs. However, the authors mention that SPAdes was initially designed for small genomes.

Is yeast too big? Can anyone recommend an assembler they use routinely/successfully for yeast?

Thanks for any advice!

[harold.smith.tarheel]

Yeast genome qualifies as small, and SPAdes should work fine.

For future reference, please submit your question as a new post (or, at the very least, do not enter it as an answer to a previous question).

[Lina F]

Thanks for the feedback -- will post the next question as a new post!