Question: Reference assisted whole-genome assembly pipeline - YEAST!
0
gravatar for palu
4.5 years ago by
palu20
palu20 wrote:

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!

ADD COMMENTlink modified 4.4 years ago by Lina F200 • written 4.5 years ago by palu20
2
gravatar for Medhat
4.5 years ago by
Medhat8.9k
Texas
Medhat8.9k wrote:

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

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Medhat8.9k

BBMap is really perfect

ADD REPLYlink written 4.5 years ago by A3.9k

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

ADD REPLYlink written 4.4 years ago by dago2.6k

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

ADD REPLYlink written 4.4 years ago by Medhat8.9k

Ok, now is clear. Thanks

ADD REPLYlink written 4.4 years ago by dago2.6k
0
gravatar for palu
4.5 years ago by
palu20
palu20 wrote:

What exactly do you mean with first and second part?

ADD COMMENTlink written 4.5 years ago by palu20
0
gravatar for Lina F
4.4 years ago by
Lina F200
Boston, MA
Lina F200 wrote:

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!

ADD COMMENTlink written 4.4 years ago by Lina F200
1

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).

ADD REPLYlink written 4.4 years ago by harold.smith.tarheel4.6k

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

ADD REPLYlink written 4.4 years ago by Lina F200
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