two pairs of short reads

[herber4]

is there a way to input more than one pair of short reads?

[rrwick]

Not directly into Unicycler, no. However, you could just combine them:

cat a_reads_1.fastq.gz b_reads_1.fastq.gz > combined_reads_1.fastq.gz
cat a_reads_2.fastq.gz b_reads_2.fastq.gz > combined_reads_2.fastq.gz

And then give them to Unicycler as a 'single' read set. This will probably work best if the two read sets have not-too-different read lengths and insert sizes.

Ryan