Author: Victor Higareda
Code Club proyect 2020: Assesign whether is variation in ASV
thinking in start a new proyect in microbiology and developt scripts
Dependencies: mothur v.1.44.1
Code club project analyzing data
License: MIT License
Author: Victor Higareda
Code Club proyect 2020: Assesign whether is variation in ASV
thinking in start a new proyect in microbiology and developt scripts
Dependencies: mothur v.1.44.1
WE will use mothur to align.seqs
Some papers related to ASV will be here
The rrnDB has [downloads] (https://rrndb.umms.med.umich.edu/static/download/) that we can use for our project, put them into data/reference
https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.6_pantaxa_stats_RDP.tsv.zip
https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.6_pantaxa_stats_NCBI.tsv.zip
https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.6_16S_rRNA.fasta.zip
https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.6.tsv.zip
Need SILVA reference alingment to align our sequences from rrnDB so that we can make sure we´re looking at a consitent region with a gene. We can get this form the [mothur wiki] (https://mothur.org/wiki/silva_reference_files/). We would like to recreate seed database
https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138.tgz
Put into this data/references
We want to get mothir to align sequences and other function /code/mothur/
Also we not to track with version control, so we should have the repository ignore the directory. Because of that lave the installation in code/README.md
and we should indicate the version of mothur dependencies. The latest [ is v.1.4 ]
)https://github.com/mothur/mothur/releases/tag/v1.44.2)
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