Should I use short-reads or long-reads?

In the past year or so, we find ourselves with multiple technology options for conducting microbial scale Whole Genome Sequencing (WGS).  We can now choose between Illumina short-read sequencing or Nanopore long-read sequencing for small genome…
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What does a sequence alignment and variant call report look like?

Our clients often use Geneious Prime to generate sequence alignment and variant call reports. They export a select list of variables including CDS, polymorphism types, codon change, amino acid change, and protein effect. We often recommend that…
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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…
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How to perform de novo assembly with PATRIC

De novo assembly is a method for generating contigs, scaffolds, or complete genomes from Next Generation sequencing reads (i.e. DNA fragments).  Some researchers use the free, online bioinformatics tool PATRIC for de novo assembly.  PATRIC…
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How to perform an NCBI nucleotide BLAST search

We often use NCBI nucleotide Blast queries to identify DNA sequences derived from Next Generation Sequencing (NGS) runs.  This brief note describes how to use the NCBI Blast algorithm and website with NGS DNA datasets. Create an NCBI Account Before…
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How to annotate a genome with Geneious

Geneious Annotations Geneious Prime includes genome annotation features and reports.  Annotation is often used to describe the structure and function of various genomic regions, such as genes, CDS's (coding sequences), exons, introns, 5'-…
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How to create Geneious variant call reports

Geneious Reports We have numerous clients who use Geneious for bioinformatics data analysis.  They use Geneious for sequence alignments of their sample datasets against reference genomes and for the interpretation of Geneious variant call…
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Geneious sequence alignment & variant calls workflow

Geneious Prime is one of many bioinformatics tools that our clients use to post-process sequencing datasets.  Geneious includes an extensive set of functions to perform sequence alignments of sample reads against reference genomes.  And it…
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What is de novo assembly?

De novo assembly is a method for constructing genomes from a large number of (short- or long-) DNA fragments, with no a priori knowledge of the correct sequence or order of those fragments. The terminology for de novo assembly is sometimes…

Sequence alignments with Geneious

Geneious Alignments Our clients often use Geneious for the alignment of sequenced samples to reference genomes. When sequencing runs are finished, our sequencers generate raw FastQ files, which typically contain millions of short DNA fragments…
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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. …
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How to read Geneious variant call reports

Reading Geneious Reports Our clients often use Geneious to generate SNP/indel variant call reports.  A truncated report is available here.  (The number of SNP's/indels in a typical report can be quite large so we only show a few records…

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 and then use one of the samples as a reference genome to compare against the remaining samples.  For example, clients may have a single control sample and several…
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How to use Phaster for bacteriophage bioinformatics

Phaster is a bioinformatics tool for analyzing bacteriophage sequencing data sets.  It generates a variety of phage identification and annotation results that are very useful for interpreting phage sequencing data.  Currently, Phaster contains…