User:Konrad U Foerstner/Tools and procedures

SNP calling

With Samtools

• Important. Base alignment quality (BAQ) is switched on per default and very (too) strict 5 Things to Know About SAMtools Mpileup

Phylogenetic trees

• Newick Utilities
• clann
• phylip
• iTOL
• PhyML

Multiple alignments

• muscle

TSS prediction

• TSSi (untested)

Whole genome alignments

• mauve

Pathway visualization

• iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
• KEGG Mapper (untested)

Transcription Terminator prediction

• TransTerm

miRNA target prediction

miRmap (untested)

Differential gene expression analysis

DESeq

• DeSeq

• Tips:
  • small count noise - sequence deeper
  • large count noise - sequence more replicates
  • if the assumption that most genes are not differentially expressed is not the case use different methods to normalize (e.g. spike-ins)

Others

• BaySEq
• edgR
• Gfold
• NoiSeq

Python

General useful libraries

• BioPython
• bx-python
• NumPy/SciPy
• numexpr Fast numerical array expression evaluator for Python and NumPy
• panda
• beautiful soup
• matplotlib
• ipython
• PyCogent
• fuzzywuzzy
• pattern
• pysam
• ete2 - For phylogenetic trees
• NetworkX
• h5py - HDF5 for Python
• PyTables
• Statsmodels - statistical models for Python
• scikit-learn - machine learning in Python
• PySB Python framework for Systems Biology modeling
• Augustus - system for building and scoring statistical models
• Bokeh - implementation of the "Grammar of Graphics"
• PyMC - Bayesian inference in Python
• matplotlib-venn - Venn diagrams in matplotlib
• gffutils

Misc

• Making matplotlib look like ggplot

Visualisation

• Circos
• ColorBrewer
• D3.js
• corrplot - R package to visualize correlations