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Software list

Below you will find a diverse toolbox comprising numerous tools for the analysis of biological sequences. Not all of the tools will be used in the course, but maybe you are interested in taking a look around to see what is currently around.

TypeNameDescriptionGUIInstallationURL
Read simulationARTIllumina, 454 and Solid read simulatoryesbiocondaLink
Read processingFastQCGenerates summary statistics and overview information for DNA and RNA seq datayesbiocondaLink
TrimmomaticAdapter clipping and quality trimming of short read datanobioconda/conda-forgeLink
Transcriptome assemblyTrinityDe novo reconstruction of transcriptomes from RNA-seq datanobiocondaLink
Genome assemblyFlye Fast and accurate de novo assembler for single molecule sequencing reads (suitable for PacBio HiFi reads)nobiocondaLink
CANU Assembler for High Noise / single molecule sequencing data (Overlap) no biocondaLink
Velvet Sequence assembler for short reads (deBruijn graph)no biocondaLink
SPades Intended for both standard isolates and single-cell MDA bacteria assemblies (deBruijn Graph)no biocondaLink
Mira Whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (Overlap)no biocondaLink
Database searchNCBI BlastHeuristic for the rapid identification of significantly similar sequences in a sequence data base using local alignmentsnobiocondaLink
NCBI Legacy BlastHeuristic for the rapid identification of significantly similar sequences in a sequence data base using local alignments. These C toolkit binaries are no longer maintained and supportednobiocoreLink
DiamondAccelerated BLAST compatible local sequence alignernobiocondaLink
Gene predictionmakerA comprehensive pipeline for genome annotationnobiocondaLink
funannotateA pipeline for gene annotation in fungal genomesnobiocondalink
TransdecoderIdentify candidate coding regions within transcript sequencesnobiocondaLink
Gene set completenessBuscoAssessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy OrthologsnobiocondaLink
fCATGene set completeness assessment tool using domain-architecture aware targeted ortholog searchesnopip link
Repeat annotationRepeat MaskerSmith-Waterman based identification and optional masking of repeats provided in a repeat databasenobiocondaLink
Genome visualizationJBrowse DesktopDesktop version of JBrowse that does not need any web server configurationyesmanuallyLink
JBrowseA browser based viewer for genomes and genome-wide annotationyesbiocondaLink
IGVIntegrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations yesbiocondaLink
igvtoolsThe igvtools utility provides a set of tools for pre-processing data files.nobiocondaLink
Structural variant detectionLumpyA general probabilistic framework for structural variant discoverynobiocondaLink
DellyA SV caller leveraging multiple signalsnobiocondaLink
MantaA SV caller leveraging multiple signalsnobiocondaLink
Structural variation comparison SURVIORA tool kit to compare, merge, and generate stats over SVs vcf filesnobiocondaLink
SAM/BAM manipulation SamtoolsA tool kit to operate with sam/bam filesnobiocondaLink
BCFTOOLS BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF no biocondaLINK
Read mapping BWAA method to align short readsnobiocondaLink
Bowtie2Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequencesnobiocondaLink
SNP caller xAtlasA method to detect SNP + indelsnobiocondaLink
RNA-Seq mapping STARA method to align RNA-Seq datanobiocondaLink
Hisat2A method to align RNA-Seq datanobiocondaLink
KallistoA method to align RNA-Seq datanobiocondaLink
TopHatA spliced read mapper for RNA-Seq nobiocondaLink
Assembly evaluationQuast Quality Assessment Tool for Genome Assemblies yes bioconda Link
RnaQuastQuality evaluation tool for assembled transcripts biocondaLink
Taxonomic AssignmentMegan interactive microbiome analysis toolno manually Link
Krona Tools Interaktive viewer for metagenome composition yes biocondaLink
Ortholog searchInParanoidPairwise ortholog search tool no manually Link
OMA Ortholog matrix project no manually Link
fDOG Targeted ortholog search tool no manually Link
Phylogenetic ProfilingPhyloProfile A browser based tool for visualizing and exploring phylogenetic profiles yes manually Link
Phylogeny reconstructionRAxML Phylogenetics - Randomized Axelerated Maximum Likelihood no bioconda Link
ProtTest3 ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at handyesmanuallyLink
Tree visualizationFigTreeGraphical viewer of phylogenetic treesyesmanuallyLink
iTOLInteractive software for the visualisation and annotation of phylogenetic treesyesWeb toolLink
mattInteractive tree visualisation, modification and topology testingyespipLink
Sequence alignmentMuscleMultiple sequence alignmentnobiocondaLink

Additional installation information

RepeatMasker

Once you have installed the repeat masker, either directly or via the installation of the maker pipeline, you will need to install the RepBase repeat library. To do so, identify the location of your RepeatMasker installation, download the current release of RepBase repeat library - note, you will have to complete a free registration before you can download the file. Move the archive file name RepBaseRepeatMaskerEdition-20170127.tar.gz into the RepeatMasker directory in 

~/anaconda/envs/compgen/share/RepeatMasker

and unpack it by typing 

tar -xzf RepBaseRepeatMaskerEdition-20170127.tar.gz

JBrowse

We will use the desktop version of JBrowse for our course. Download the version that matches your operating system from the JBrowse web sites and follow the installation guidelines provided with the software.

Databases

Databases and web tools: