Linux and Git

Git git Linux linux

Regular Expressions

Basics basic-regexp In Python python-regexp

R

Simple tasks R-basics Clustering R-clustering Data frame R-dataframe Library dplyr R-dplyr File Read/Write R-excel Library ggplot R-ggplot Plot functions R-plotting Regression analysis R-regression String Processing R-string Vectors R-vectors

Bioconductor

DESeq R-DESEQ Annotate R-annotate Ape R-ape Biostrings R-biostrings Rcytoscape R-cytoscape edgeR R-edgeR Graph R-graph Limma R-limma Library IRanges R-ranges Shortread R-shortread Excellent tutorials R-tutorials

Python and Biopython

Biopython biopython Python Basics python

Kmer Processing

DSK dsk Jellyfish jellyfish KMC kmc

Read Compression

DSRC dsrc

Genome Assembly - Short Reads

Allpaths-LG allpaths Bcalm bcalm Meraculous meraculous SOAPdenovo soapdenovo Spades spades

Genome Assembly - Long/Hybrid Reads

Canu canu DBG2OLC dbg2olc Falcon falcon LorDec lordec Miniasm miniasm Reckoner reckoner

Sequence Mapping

BLAST BLAST DALIGNER DALIGNER MUMmer MUMmer STAR STAR BLASR blasr Bowtie bowtie BWA bwa Exonerate exonerate HMMer hmmer Minimap minimap Samtools samtools

Multiple Alignment and Clustering

CD-hit cd-hit MUSCLE muscle

Phylogeny

RAxML RAxML Fasttree fasttree

RNAseq

DESeq DESEQ Kallisto kallisto Maker maker Salmon salmon SOAPdenovo-trans soapdenovo-trans Trinity trinity

Microbial Genomics

USEARCH USEARCH Kraken kraken MEGAhit Assembler megahit Mothur mothur QIIME qiime

CRISPR Analysis

tRNA Analysis

Aragorn aragorn tRNAscan-SE tRNAscan-SE

miRNA Analysis

mfold/UNAfold mfold Mirnafold mirnafold Targetscan targetscan

Databases

NCBI BLAST DB blastdb ENSEMBL ensembl IMG database jgi-img Mirbase mirbase RCSB rcsb UCSC ucsc Uniprot uniprot

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