viral amplicons single-end assembly

Question

[monia.ardhaoui]

I would like to assemble single-end data generated from viral amplicons. I used SPades but it doesn't work, and it required paired-ends data any suggestions please?

[GenoMax]

You can try tadpole.sh from BBMap suite. A guide is available here.

[5heikki]

SPAdes does not require paired reads..

[monia.ardhaoui]

what option shall I use for single*end reads?

[JC]

use the -s option

[Hamid Ghaedi]

Try Genome Detective and enjoy its simplicity in submitting a job and getting back a detailed result.

[monia.ardhaoui]

Thank you, but I need to do it by command line:)

[gb]

You sure there is no reference available? If there is, BWA or bowtie.

Answer 1

[Mensur Dlakic]

When you type spades.py without any arguments, it will give you a long list of options. What's relevant for you:

Input data:
  --12 <filename>             file with interlaced forward and reverse paired-end reads
  -1 <filename>               file with forward paired-end reads
  -2 <filename>               file with reverse paired-end reads
  -s <filename>               file with unpaired reads

Another option is megahit, also options that are relevant for you:

  Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)
    -1                       <pe1>          comma-separated list of fasta/q paired-end #1 files, paired with files in <pe2>
    -2                       <pe2>          comma-separated list of fasta/q paired-end #2 files, paired with files in <pe1>
    --12                     <pe12>         comma-separated list of interleaved fasta/q paired-end files
    -r/--read                <se>           comma-separated list of fasta/q single-end files