Question: Does Squid work on ISO-seq?

[zeeev]

We have ISO-seq alignments using gmap2, Will squid run on these data?

[Congm12]

The current implementation assumes paired end reads with inward orientation. And that information is used in distinguishing discordant reads with concordant, which affects genome segmentation but not rearrangement. For ISO-seq, the reads setting should be different, and requires a different implement of parsing reads. So short answer is I don't think it will run correctly on ISO-seq now. But I would like to look into ISO-reads alignment, and implement parsing long reads in the future.