... We created a set of programs called gargammel that can simulate the reads once you have the fasta file of the genome:
[gargammel on github]
[here is the paper]
For simulating demographies, I have been using msprime.
: https://academic.oup.com ...
... There are different layers of raw data way before demultiplexing:
1. The files at the most basic layer are raw images, those are massive.
2. After image analysis, you have intensity for each cluster, those are normally in .cif format. They do not contain bases but raw intensity.
3. After baseca ...
... This post is between a comment and a response. I work a lot with ancient DNA where fragments are very short (e.g. 40bp). This entails that even for a paired-end run you constantly have to deal with "single-end" reads (merged paired-end) and genuine paired-end data. The logic was getting very convolu ...