This is a test version of Biostars. For the public version, visit https://www.biostars.org.
evaluation of sequencing coverage depth

Dear All,

At the outset, I would like to point out that I am an amateur in the field of NGS.

I've performed sequencing of prokaryotic genome (Alcaligenes faecalis with use of short (Illumina) and long reads (Nanopore). My goal is to fully resolve genome and mobilome structures with use of hybrid assembly (Unicycler).

Here comes the stupid question - how can I determine coverage depth? I should check FASTQ/FAST5 from both technologies separately?

thanks in advance,

Piotr

genome sequencing next-gen assembly
• 1,946 views • link
written by piotr.majewski • piotr.majewski

You can align your reads back to the assembly you have (referred to in a separate question). That should allow you to check depth at every base (use mosdepth or samtools depth) using the alignment files you get. Use minimap2 for alignment with long reads and any other NGS aligner for Illumina short reads.

• 0 views • link
written by GenoMax GenoMax

1 answer

PS

I'm shall ask another question here. I do not want to make a mess with multiple topics.

After hybrid assembly, I've received 3 contigs

1 (4.3 Mb) - genome, circular (via Geneious) 2 (43.5 kb) - plasmid?, circular (via Geneious) 3 (11 kb) - ?

how can I be sure that contigs 2&3 stands for plasmids? or maybe single plasmid divided into 2 contigs?

• 0 views • link
written by piotr.majewski • piotr.majewski

This is not related to your original question so delete the post here and ask as a separate question.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this