Tools

m

Go Enrichment

a

SOP: Identifying enriched biological themes in gene sets

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Categorizer

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geneSCF

BLAST2GO

Can use custom background gene list

Online services

AMIGO Term Enrichment

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Gene Venn Diagram

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FASTQ quality control

FASTX-Toolkit

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FASTQC

r

Download packageLaunch desktop FastQC using the .bat file

FastQ Screen

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Transcriptomes

BBMap

a

STAR (for 454 reads)

r

1.Generate genome indexSTAR --runMode genomeGenerate --genomeDir </path/to/GenomeDir> --genomeFastaFiles </path/to/genome/fasta1> --runThreadN <#> --sjdbGTFtagExonParentTranscript </path/to/genomeGFF> 2. Run alignmentSTAR --genomeDir </path/to/GenomeDir> --readFilesIn </path/to/read1> --runThreadN <#> http://pipe-star.readthedocs.io/en/latest/explain_star.html

a

User manual

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Mapping RNA-seq Reads with STAR

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Google Group

a

Subtopic

SortMeRNA

a

Tophat

Bowtie2

r

1. Index reference genomebowtie2-build <genome.fa> <index name> 2. Map reads to reference genome indexbowtie2 -p <# cpu> -x <index name> <fastq file> > <output file>

a

BWA

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GMAP

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Motif discovery

HOMER

a

Coding sequence prediction

TransDecoder

a

Useful commands

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Phylogenetic analysis

PhyML

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MEGA7

CAFE v4

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Tutorial

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Version using DIAMOND BLAST

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r8s

Notes on installation

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PAML

a

Tutorial

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Orthology

OrthoFinder

a

Mirlo

a

Proteinortho5

r

OneNote

a

Software

Misc

Linuxbrew

a

Diamond

r

$ diamond makedb --in nr.faa -d nr $ diamond blastx -d nr -q reads.fna -o matches.m8

a

User manual

a

MagicBlast

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Picard

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Install Java 1.8

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Installation

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IGV

a

Cufflinks

InterProScan

r

How to downloadHow to run InterProScan (command line)

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Miniconda

a

Should install Miniconda2, since some programs need Python 2.7

GeneValidator

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Retrotransposons

LTRharvest

a

LTRdigest

a

LTRsift

a

Non-coding RNA

RNAmmer

Need HMMER 2.3.2