Upload your sequence file in FASTQ format via Sequences > Upload Sequence File. If you have paired-end information then two files should be uploaded corresponding to sequences read in each direction. Alternatively you can retrieve your data directly from a web-server, if you have been supplied a web address (URL) for your sequence. Choose Sequences > Retrieve Sequence File from Remote Server and post the URL.
Once the sequence file has been uploaded, ensure it is set to the correct version of FASTQ - for most recent sequencing runs (2009 onwards) Illumina 1.3+ is the best choice.
Select Mapping > Perform Mapping against Reference Sequence
Under Sequence File choose your FASTQ file. If you have paired-end data select the second FASTQ file under "Second Sequence File". In that case tick "paired-end mode".
Select a reference genome from the drop-down.
Give your alignment a descriptive name (e.g. "strain XX mapped against K-12") to help you find it later
Check other settings and click "Perform Alignment"
Click the link for the newly-created alignment.
Click "Start Job"
Refresh the page until "Finished" is displayed. This can take between a few minutes and half an hour depending on the size of the dataset.
Click on the link to the alignment.
To view SNPs, click "Table of SNPs".
A list of SNPs will be shown, displayed with predicted change of amino acid sequence if the SNP falls within an annotated gene.
