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What does a sequence alignment and variant call report look like?

Our sequence alignment and variant call reports are generated by a tool called Geneious Prime. We export a select list of variables including CDS, polymorphism types, codon change, amino acid change and protein effect. There is a wealth of…
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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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Trimming Illumina adapter sequences

Adapter Sequences During the library preparation process, Illumina adapter sequences are annealed to sequencing reads. The adapter sequences are required for attaching reads to flow cells and for attaching indexes to reads.  When sequencing…
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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…
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What are unmapped reads?

Save Unmapped Reads One of the most common activities we perform is the sequence alignment of sequenced bacterial samples against known reference genomes.  The alignment process generates two types of output: mapped reads and unmapped reads.…
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How to read FastQ files

FastQ File Format Illumina sequencing instruments generate FastQ files when a sequencing run is finished.  FastQ files are the starting point for all downstream bioinformatics data analysis.   The file name suffix for a FastQ file is:…