SPADES assembly failed, unequal amount of reads

Question

[kingcohn]

I am attempting to assemble a novel insect genome using several assemblers (abyss, spades, minia...etc). I've preprocessed the raw paired-end fastq files following the Palumbi Lab's: Simple Fool's Guide, which uses tools in the fastqtoolkit like quality trimmer, duplicate counter...etc. I also have two read versions, from different lanes, which I preprocess similarly and then concatenate. However, after running abyss and spades I am getting errors that my files contain unequal amount of reads. I just downloaded BBMap and will try to preprocess using this, but would like some advice. Thanks

[Medhat]

I think you you used for trimming tools that are not aware of paired reads, so I think after using BBMap or skewer then you will not face the problem

Answer 1

[harold.smith.tarheel]

Trimming produces orphan (unpaired) reads. SPADES (and most other assemblers) expect all reads to be paired (and usually in the same order). Your data can be fixed using BBMap's repair.sh function.

[Roy]

Actually, SPAdes will accept unpaired reads, but they need to be provided separately using the -s option.

[harold.smith.tarheel]

That's correct, but will still require the OP to split paired and orphan reads into separate files (which can be done with the tool I recommended).