,

What is the read length for short-read genome sequencing?

We use an Illumina MiniSeq for our short read sequencing runs.  The paired-end short read lengths are always 2 x 150bp = 300bp.  The library prep protocols are designed to fragment DNA into 150bp reads, and paired-end read runs combine two…
,

How to generate a complete genome with hybrid assembly

Introduction In this article we'll describe the Unicycler hybrid assembly pipeline.  Unicycler is designed primarily for de novo assembly of bacterial genomes and includes the major steps required for hybrid assembly of sequenced microbial…

What are paired-end reads?

Many sequencing library preparation kits include an option to generate so-called "paired-end reads".  In "short-read" sequencing, intact genomic DNA is sheared into several million short DNA fragments called "reads".  Individual reads can…
,

What is sequencing coverage?

Coverage is defined as the number of sample nucleotide bases sequence aligned to a specific locus in a reference genome. The easiest way to explain this is with a real sequenced bacterial sample that has been aligned to the reference genome…
,

How to find a reference genome

The goal of many sequencing projects is to identify polymorphisms and mutations in sequenced samples.  These often include SNP's, indels, chromosomal rearrangements and various kinds of spontaneous or induced changes in nucleotide sequence.…

Can I use one of my sequenced samples as a reference genome?

We are often asked if clients can submit several samples at once for sequencing (i.e. multiplex runs) and then use one of the samples as a reference genome for comparison with the remaining samples.  For example, clients may have a single control…