Question: Bacterial de novo genome assembly
1
gravatar for Paul
2.5 years ago by
Paul80
India
Paul80 wrote:

I have pair end Fastq files from illumina (Fast1.fastq and Fast2.fastq). Now, how should I proceed further with de-novo genome assembly? I'am completely new to this field of assembling genome sequences? Which open-end tools can be used?

Please help me with the tools and tutorials which can be used for de-novo assembly of sequences.

ADD COMMENTlink modified 2.5 years ago by Brian Bushnell16k • written 2.5 years ago by Paul80
1

Hi , You can read this article to start : http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017915

Best

ADD REPLYlink written 2.5 years ago by Titus900

what did you try? There are plenty of tutorials out there. What organism do you have? Bacteria?

ADD REPLYlink written 2.5 years ago by dago2.5k

Yes it is for Bacteria

ADD REPLYlink written 2.5 years ago by Paul80

I think we need a little more details to help you. If you want to learn general procedures, well the literature is there for you as it was for us!

ADD REPLYlink written 2.5 years ago by Macspider3.0k

Ya general procedures with the softwares available

ADD REPLYlink written 2.5 years ago by Paul80
1

I spoke with friend who work on meta genomic Bacteria data and to him the most use software for bacteria assembly is SPADes.

Best

ADD REPLYlink written 2.5 years ago by Titus900
5
gravatar for Brian Bushnell
2.5 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

If you download the BBMap package, there is a (hopefully) helpful guide in bbmap/docs/guides/PreprocessingGuide.txt

For isolate bacterial assembly with SPAdes, I recommend:

1) Adapter-trimming (you can do quality-trimming at the same time; I suggest a low cutoff, such as Q10)

2) Artificial contaminant filtering

3) Human contaminant removal

4) Error correction

5) Paired-read merging

...then assemble with SPAdes, using both the merged and unmerged reads.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Brian Bushnell16k
1

check assembly quality with QUAST

ADD REPLYlink written 2.5 years ago by dago2.5k

Thanks a lot for the detailed explanation. Is there any best tool to do the bacterial genome assembly in windows?

ADD REPLYlink written 2.5 years ago by Paul80
1

You will have so much more options if you use Linux... Windows is a great operating system, but not for bioinformatics.

ADD REPLYlink written 2.5 years ago by WouterDeCoster41k

Look these: Best software to assemble bacterial genomes And also a list of tools available is here. You can check the one that work in windows amongst them.

ADD REPLYlink written 2.5 years ago by dago2.5k
1

I don't know of many off-hand. CLC Genomics Workbench will do assembly, but it isn't free. It's a decent one-stop-shop for pretty much everything however (and is GUI based if you're commandline averse).

ADD REPLYlink written 2.5 years ago by Joe14k
2
gravatar for Joe
2.5 years ago by
Joe14k
United Kingdom
Joe14k wrote:

The general procedure I follow is:

  1. Quality control your data before you do anything else. FastQC is a go-to tool for this.
  2. Trim sequences to remove adapters etc if necessary. (See Seqtk, sickle, cutadapt, trimgalore and other such tools)
    • It may make sense to filter the reads out at this stage and throw away anything that is garbage.
  3. Assemble (See SOAP, Velvet, SPAdes)
  4. Re-map the reads to get coverage statistics etc (optional but advised). (See, Bowtie2, BWA, Qualimap etc)
  5. Optionally, if you have published reference genomes, you may wish to reorder contigs (See progressiveMauve/Mauve)
ADD COMMENTlink written 2.5 years ago by Joe14k
1

Not to forget that you can use a reference assisted assembly if you consider that a nice reference genome can be used for this purpose

ADD REPLYlink written 2.5 years ago by Antonio R. Franco4.1k

Indeed :) OP asked for de novo specifically, but if reference guided is desirable I believe programs like MIRA will do it.

ADD REPLYlink written 2.5 years ago by Joe14k

Many other programs do it. In particular, Velvet and SOAP can use reference genomes to assist a de novo assembly.

In my hands. the using of a trusted reference genome for assisting a de novo assembly, gave better results than a de novo assembly that was processed by Mauve afterwards

ADD REPLYlink written 2.5 years ago by Antonio R. Franco4.1k
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