How to include unpaired reads in assembly?

Question

[Nikhil Chaudhary]

Hello Community,

I am using SPAdes for denovo assembling from paired-end Illumina reads. I have assembled from HQ paired end reads with very good results. But I would like to know how (if) I should incorporate unpaired reads in my assembly. I have tried concatenating the unpaired reads with the contigs from the paired reads and the results were not good. Any guides on whether (and how, if yes) to include unpaired reads in the assembly.

Nikhil

[jigarnt]

Getting this error:

 /Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 --careful --only-assembler --pe<#>-12 <euro_plasmid_r1_paired.fastq euro_plasmid_r2_paired.fastq=""> --pe<#>-s1 <euro_plasmid_r1_unpaired.fastq> --pe<#>-s2 <euro_plasmid_r2_unpaired.fastq> -o Euro_plasmid_spades_output
-bash: syntax error near unexpected token `newline'

what is wrong with the command?

Answer 1

[Lesley Sitter]

I don't have evidence that my assemblies were improved by doing this but I do incorporate unpaired reads because they still contain 100 bases of information that might extend a contig or bridge a gap somewhere (i'm using data that was randomly digested using a Nextera XT kit, so in my case it makes sense to do this, this might not be the case in your project idk)

To do this in the help of SPAdes it states;

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
--s<#>          <filename>      file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)

So you can just add the command -s <read_file>

Or if you have more than 1 unpaired read file use --s1 <read_file_1> --s2 <read_file_2> --s(n) <read_file_n>

[Nikhil Chaudhary]

Yes, it works ! Thank you.