README

A pipeline for building a phylogenetic tree from the full length 16S sequences

The pipeline contains three steps.

1. Multiple sequence alignment (http://mafft.cbrc.jp/alignment/software/)

2. Phylogenetic Analysis & generate the phylogenetic tree (http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html)

3. Write the tree in pdf (https://github.com/rambaut/figtree)

==Sequence header format==

Note: Replace illegal characters in headers to make them valid sequence header.

Illegal characters in headers are: tabulators, carriage returns, spaces, ":", ",", ")", "(", ";", "]", "[", "'"

hint: tr -d '[:,)(;[]]'''') ( tr deletes the specified characters above, including the single quote, from the input string)

A sample batch submission script

aws batch submit-job \
  --job-name nf-phylogenetic-tree \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-phylogenetic-tree, \
"--project", "TEST", \
"--fasta", "s3://genomics-workflow-core/Results/phylogenetic_tree/inputs/3B.fasta", \
"--outdir", "s3://genomics-workflow-core/Results/phylogenetic_tree" "

The tree in pdf is available at

s3://genomics-workflow-core/Results/phylogenetic_tree/TEST/pdf/

View and edit phylogenetic trees

FigTree:

http://tree.bio.ed.ac.uk/software/figtree/

List of tree visualization tools

https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software