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?
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
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version 2.3.6
You can try
tadpole.shfrom BBMap suite. A guide is available here.SPAdes does not require paired reads..
what option shall I use for single*end reads?
use the -s option
Try Genome Detective and enjoy its simplicity in submitting a job and getting back a detailed result.
Thank you, but I need to do it by command line:)
You sure there is no reference available? If there is, BWA or bowtie.