Question: Need help regarding assembler
0
gravatar for popayekid55
14 days ago by
popayekid5530
popayekid5530 wrote:

Hi all,

I am very new to genome assembly. I have got 4 data for a genome of size 50M. Data what i have are, illumina short insert lib (200-500), long insert lib (300-600), mate pair (3-5kb) and nanopore (yet to receive). Kindly suggest which assemblers to use?? which data to use what stage (assembly, scaffolding or gapclosure)?? how do i get best kmer apart from kmergenie? Any other kmer identifier?

Detailed input is much appreciated.

Right now i am thinking of spades and idba_ud for assembly using both short and long insert together. Further need some assistance.

Thank you

next-gen genome • 206 views
ADD COMMENTlink modified 12 days ago by Ram12k • written 14 days ago by popayekid5530
1

Please elaborate on the species, or at least kingdom of life to which your species belongs. Also, does a reference genome already exist for this species?

There are many options for assembly, including:

  • ABySS
  • Velvet, which allows you to have analyse multiple read-lengths together, and VelvetOptimiser, which assists you in identifying the ideal K-mer size

ADD REPLYlink written 13 days ago by Kevin Blighe7.3k

Data what I have is 150 x 2. Data is for green algae. I thought velvet is for max read length of 100 x 2. I have already started with abyss .. K from kmergenie.. Also trying idba-ud as it is a multi k mer assembler. What other options ??

No reference available..

ADD REPLYlink modified 13 days ago • written 13 days ago by popayekid5530
1

Velvet can tolerate any read lengths. It was designed to cater for short-read assembly, but it accepts a mixture or either of both. To be honest, I don't believe that any genome can be faithfully assembled from short reads and I think that using short reads is sacrificing precision of the assembly a bit too much - a personal opinion based on my knowledge of the assembly algorithms.

ADD REPLYlink written 13 days ago by Kevin Blighe7.3k

Thank you. I will try with velvet. Any luck on scaffolding and gapcloser .

ADD REPLYlink written 12 days ago by popayekid5530
1

I'd suggest unicycler, heard lots of good things about it.

ADD REPLYlink written 13 days ago by WouterDeCoster23k

Unicycler is a exclusive bacterial assembler. Mine is algal sample. I could try this for a bacterial sample. Thank you for suggestion. Are there any specific for algal

ADD REPLYlink modified 13 days ago • written 13 days ago by popayekid5530

Have you tried SPAdes?

ADD REPLYlink written 11 days ago by Sej Modha2.2k

I have already used spades, abyss and idba_ud

ADD REPLYlink written 11 days ago by popayekid5530

If you already have a bunch of assemblies then you should think about consolidating them using GARM or equivalent.

ADD REPLYlink written 11 days ago by Sej Modha2.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 607 users visited in the last hour