https://github.com/k8hertweck/hertwecklabsops

Standard operating procedures for generic phylogenetics methods.
https://github.com/k8hertweck/hertwecklabsops

teaching

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Standard operating procedures for generic phylogenetics methods.

• Host: GitHub
• URL: https://github.com/k8hertweck/hertwecklabsops
• Owner: k8hertweck
• Created: 2014-10-31T20:04:00.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2017-05-25T19:24:29.000Z (over 7 years ago)
• Last Synced: 2023-04-04T08:51:58.260Z (over 1 year ago)
• Topics: teaching
• Language: Shell
• Size: 21.5 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

        
HertweckLabSOPs

================

Standard operating procedures for generic bioinformatics methods.

These files are short cheat sheets for my preferred methods to run in a bash shell or in R; they assume a basic understanding of the command line (see [my website](https://sites.google.com/site/k8hertweck/resources/bioinformatics-skills) for a general overview and an explanation of installing and running these programs). Each file is not meant to be run in its entirety; instead, extract the script for your particular method of interest and paste into the command line or another script, replacing XXX (described at the beginning of each document) with your filenames. 

##Data parsing

* `extractSequences.md` includes a few ways to extract a subset or reorder sequences in a fasta file

##Phylogenetic analysis (`phylogenetics/`)

Scripts assume nucleotide data, unless amino acid (protein) data is otherwise specified. If you are starting with unaligned nucleotide data, you will likely consult the files in the following order:

* `sequenceAlign.md` multiple sequence alignment

* `MLphylogenetics.md` maximum likelihood tree inference

* `treeViz.md` tree visualization

##Next-generation sequencing assembly (`ngs/`)

* `sequenceQC.md` filtering raw next-generation sequencing reads for quality

* `plastomeAssembly.md` assembling the chloroplast genome from next-generation sequencing data

Additional (but less often used) scripts can be found in `miscPrograms.md`