Metagenomic data assembly.

Question

[faizansaleem1992]

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.

Answer 1

[shenwei356]

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.

[Brian Bushnell]

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.

Answer 2

[lakhujanivijay]

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

Of course you need both R1 and R2 for assembly.

[faizansaleem1992]

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 ?

Answer 3

[Brian Bushnell]

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

[faizansaleem1992]

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.

[Medhat]

the link @Brian posted contains example

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

Answer 4

[shenwei356]

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