Merging multiple runs of the same samples

Question

[bioinformaticssrm2011]

We performed three sequencing runs for the same set of samples, using the same DNA, library preparation, and sequencing protocols. What would be the best approach to handle multiple runs? Should we concatenate the runs into a single dataset before proceeding with assembly?

Answer 1

[GenoMax]

Depending on assembler you may be able to provide multiple files for the same sample in proper order as input (i.e make sure R1 files match R2 files in input order).

From SPAdes manual:

In file pairs. In this case left and right reads are placed in different files and must go in the same order. I.e. for every left read at line X in the first file the corresponding right read from the pair must be at line X in the second file.

You could also concatenate the files into a single pair of files, if you prefer.