Tutorial: Comprehensive Genome Analysis Service

Overview

This set of short videos provides a step-by-step demonstration of using the PATRIC Comprehensive Genome Analysis service to assemble, annotate, and provide a basic comparative analysis of close relatives to a bacterial genome.

  1. Submitting a job using reads (13:08)

  2. Submitting contig files (3:36)

  3. Full genome report (13:06)

  4. Job results (11:22)

  5. Assembly results (6:13)

  6. Annotation results (8:50)

  7. Viewing your genome (8:05)

  8. Finding help and citing PATRIC (6:51)

Using the Comprehensive Genome Analysis Service

Links to the videos are provided below. They can also be viewed in order in the PATRIC YouTube channel playlist. Relevant references are provided at the bottom of this page.

1. Submitting a job using reads (13:08)

2. Submitting contig files (3:36)

3. Full genome report (13:06)

4. Job results (11:22)

5. Assembly results (6:13)

6. Annotation results (8:50)

7. Viewing your genome (8:05)

8. Finding help and citing PATRIC (6:51)

References

  • Antipov, D., et al., plasmidSPAdes: assembling plasmids from whole genome sequencing data. bioRxiv, 2016: p. 048942.

  • Bankevich, A., et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 2012. 19(5): p. 455-477.

  • Brettin, T., et al., RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific reports, 2015. 5: p. 8365.

  • Davis, J.J., et al., PATtyFams: Protein families for the microbial genomes in the PATRIC database. 2016. 7: p. 118.

  • Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 2004. 32(5): p. 1792-1797.

  • Koren, S., et al., Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome research, 2017. 27(5): p. 722-736.

  • Krueger, F., Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. URL http://www. bioinformatics. babraham. ac. uk/projects/trim_galore/.(Date of access: 28/04/2016), 2012.

  • Nurk, S., et al., metaSPAdes: a new versatile metagenomic assembler. Genome research, 2017. 27(5): p. 824-834.

  • Ondov, B.D., et al., Mash: fast genome and metagenome distance estimation using MinHash. Genome biology, 2016. 17(1): p. 132.

  • Overbeek, R., et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res, 2014. 42(Database issue): p. D206-14.

  • Stamatakis, A., RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 2014. 30(9): p. 1312-1313.

  • Vaser, R., et al., Fast and accurate de novo genome assembly from long uncorrected reads. Genome research, 2017. 27(5): p. 737-746.

  • Walker, B.J., et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS one, 2014. 9(11): p. e112963.

  • Wick, R.R., et al., Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS computational biology, 2017. 13(6): p. e1005595.