Badread

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What happens when I use a mean fragment length bigger than the largest contig, with zero std.dev?

baraaorabi

**Describe the bug** Hello, I have attempted to use badread to create a custom error model based on read data. I wanted to compare badread simulated samples using a custom...

evantroendle

Documentation on post processing of simulated sequences

1

Could you add additional documentation on the recommendations for post processing of the simulated sequencing data. Following simulation of sequencing data, fastq or fastq.gz files were filtered and trimmed using...

ahfitzpa

I'm trying to generate multiple transcriptomic datasets in parallel with different parameters (error model, coverage/depth, and sequence identity), however, Badread consumes a lot of memory while doing this and occasionally...

RDorney

Runtime improvement

1

Hi, First, thanks for this soft. I've been running a lot of badread runs for a project and while waiting for the soft to finish, I found it fun to...

jsgounot

How to handle PacBio simulated reads before mapping

2

Hello @rrwick, I experienced some poor mapping performance with Minimap2 for reads simulated using the pacbio2016 (only changing depth, mean sequence identity, all other settings as default). I noticed it...

RDorney