Question: Metagenomic data assembly.
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gravatar for faizansaleem1992
2.3 years ago by
faizansaleem199230 wrote:

Hello, I have obtained two files through illumina shotgun sequencing forward and reversde and would like to perform assembly of my metadata. kindly suggest an easy to use metagenomic assembler with tutorial. and also do i have to use both type of reads for the assembly purpose or one file will be enough ? thank you.

ADD COMMENTlink modified 2.3 years ago by shenwei3564.5k • written 2.3 years ago by faizansaleem199230
1
gravatar for shenwei356
2.3 years ago by
shenwei3564.5k
China
shenwei3564.5k wrote:

Yestoday (2016-12-30), a manuscript (not peer-reviewd) titled "Evaluating Metagenome Assembly on a Complex Community" from C. Titus Brown compared IDBA-UD, SPAdes and MEGAHIT.

ADD COMMENTlink written 2.3 years ago by shenwei3564.5k

I also find Megahit to be much faster and use far less memory compared to Spades, though Spades assemblies have moderately better continuity, when it finishes. But Spades is not currently suitable for metagenomes beyond very simple ones. Generally, resources permitting, I recommend running both Spades and Megahit and using the Spades assembly if it finishes, and otherwise the Megahit assembly. But if you have to pick just one, it's Megahit.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Brian Bushnell16k
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gravatar for Vijay Lakhujani
2.3 years ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

Check out metavelvet - http://metavelvet.dna.bio.keio.ac.jp/

Of course you need both R1 and R2 for assembly.

ADD COMMENTlink written 2.3 years ago by Vijay Lakhujani4.0k

Vijay thanks alot for specifying one problem for me. can you please tell me that will there be one contig file after assembly by using r1 and r2 or multiple file i mean one for each ?

ADD REPLYlink written 2.3 years ago by faizansaleem199230
0
gravatar for Brian Bushnell
2.3 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

I recommend Megahit. It's quite easy to use.

ADD COMMENTlink written 2.3 years ago by Brian Bushnell16k

Thank you Brian. I was also thinking about using megahit if possible can you please provide a tutorial of megahit ? It will be a great favour to me.

ADD REPLYlink written 2.3 years ago by faizansaleem199230

the link @Brian posted contains example

megahit/megahit -1 SRR341725_1.fastq.gz -2 SRR341725_2.fastq.gz -o SRR341725.megahit_asm

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Medhat8.2k
0
gravatar for shenwei356
2.3 years ago by
shenwei3564.5k
China
shenwei3564.5k wrote:

IDBA-UD has competitive performance. Sorry I forgot evidences...

ADD COMMENTlink written 2.3 years ago by shenwei3564.5k
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