a guide to microbioma analisis

8/10/2019 a guide to microbioma analisis

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Accompanying the paper:

Beginner’s guide to comparative bacterial genome analysis using next-

generation sequence data

David J. Edwards, Kathryn E. Holt

BMC Microbial Informatics, 2013

Last updated March 2013

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1.1 Downloading E. coli sequences for assembly .................................................... 2

1.2 Examining quality of reads (FastQC) ................................................................. 2

1.3 Velvet – assembling reads into contigs .............................................................. 4

1.3.1 Using VelvetOptimiser to optimise de novo assembly with Velvet .............. 6

1.4 Ordering contigs against a reference using Mauve ........................................... 7

1.4.1 Viewing the ordered contigs (Mauve) ........................................................ 10

1.4.2 Viewing the ordered contigs (ACT) ........................................................... 13 1.5 Mauve Assembly Metrics – Statistical View of the Contigs .............................. 15

1.6 Annotation with RAST ...................................................................................... 15

1.6.1 Alternatives to RAST ................................................................................. 19

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2.1 Downloading E. coli genome sequences for comparative analysis ................. 20

2.2 Mauve – for multiple genome alignment .......................................................... 21

2.3 ACT – for detailed pairwise genome comparisons .......................................... 24

2.3.1 Generating comparison files for ACT ........................................................ 24

2.3.2 Viewing genome comparisons in ACT ...................................................... 27

2.4 BRIG – Visualizing reference-based comparisons of multiple sequences ....... 29

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3.1 PHAST – for identification of phage sequences ............................................... 34

3.2 ResFinder – for identification of resistance gene sequences........................... 34

3.3 Multilocus sequence typing .............................................................................. 34

3.4 PATRIC – online genome comparison tool ...................................................... 34



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blastn -query SRR292770_single.fasta -dbNC_011748.fasta -evalue 1 -task megablast -outfmt 6> SRR292770_NC_011748.crunch

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a guide to microbioma analisis

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