Successfully reported this slideshow.

Viral biodiversity in rodents

0

Share

Upcoming SlideShare
29 Mammalian Genomes
29 Mammalian Genomes
Loading in …3
×
1 of 15
1 of 15

Viral biodiversity in rodents

0

Share

Download to read offline

I was invited to give a short presentation about the tools that I use for my research in Cayenne, French Guiana (sickle, velvet, digital normalization (khmer), krona, awk and others).

I was invited to give a short presentation about the tools that I use for my research in Cayenne, French Guiana (sickle, velvet, digital normalization (khmer), krona, awk and others).

More Related Content

Related Books

Free with a 14 day trial from Scribd

See all

Related Audiobooks

Free with a 14 day trial from Scribd

See all

Viral biodiversity in rodents

  1. 1. Does human perturbation affect the viral biodiversity of rodents? nacho caballero pasteur cayenne
  2. 2. Collect biological samples
  3. 3. Isolate the viruses
  4. 4. Sequence viral cDNA
  5. 5. Analyze read quality FastQC
  6. 6. Trim low-quality base pairs sickle - github.com/najoshi/sickle
  7. 7. Split reads into k-mers k
  8. 8. Remove redundant reads number of nucleotides with that coverage 0 10 coverage 100
  9. 9. Remove redundant reads digital normalization (khmer) number of nucleotides with that coverage 0 10 coverage 100
  10. 10. Assemble reads into contigs velvet - www.ebi.ac.uk/~zerbino/velvet/
  11. 11. Align contigs to known sequences blastn - blastx - tblastx NCBI bit.ly/vipr_download viprbrc.org
  12. 12. Classify alignments by taxonomy krona
  13. 13. zsh (globbing, renaming) awk sed join sort grep cut R Powerful file manager Small tools that do one thing well Statistics and data reshaping
  14. 14. Does human perturbation affect the viral biodiversity of rodents? nacho@bu.edu

×