Please list the software you require on the course virtual machine.
| Software Name | Version | Link | Session |
|---|---|---|---|
| wget | 1.2.1 | https://www.gnu.org/software/wget/manual/wget.html | intro to unix |
| artic-ncov19 (conda env) | latest | https://github.com/artic-network/artic-ncov2019.git | sars-cov-2 |
| pangolin (conda env) | latest | https://github.com/cov-lineages/pangolin | sars-cov-2 |
| civet (conda env) | latest | https://cov-lineages.org/resources/civet/updating.html | sars-cov-2 |
| spear (conda env) | latest | https://github.com/m-crown/SPEAR | sars-cov-2 |
| usher (conda-env) | latest | https://usher-wiki.readthedocs.io/en/latest/QuickStart.html#quick-install | sars-cov-2 |
| ncov2019-artic-nf (nextflow) | latest | https://github.com/connor-lab/ncov2019-artic-nf | sars-cov-2 |
| trim_galore | latest (0.6.7) | https://github.com/FelixKrueger/TrimGalore | sars-cov-2 |
| minimap2 | latest (2.2.4) | https://github.com/lh3/minimap2 | sars-cov-2, BASH_scripting |
| samtools | latest | http://www.htslib.org/download/ | sars-cov-2, BASH_scripting Coverage_plots NGS_file_formats |
| ivar | latest (1.3.1) | https://github.com/andersen-lab/ivar | sars-cov-2 |
| lofreq | lofreq3 | https://github.com/andreas-wilm/lofreq3 | sars-cov-2 |
| snpeff | latest | http://pcingola.github.io/SnpEff/ | sars-cov-2 |
| mafft | latest | https://mafft.cbrc.jp/alignment/software/ | sars-cov-2, Multiple Sequence Alignment |
| iqtree2 | latest (2.2.0) | http://www.iqtree.org/#download | sars-cov-2, Molecular Phylogeny |
| R | latest | https://cran.r-project.org | sars-cov-2 |
| python3 | latest | https://www.python.org/downloads/ | sars-cov-2 |
| FigTree | latest | https://github.com/rambaut/figtree/releases | sars-cov-2 |
| seqtk | latest | https://github.com/lh3/seqtk | sars-cov-2 |
| bbmap | latest | https://sourceforge.net/projects/bbmap/ | sars-cov-2 NGS_file_formats |
| weeSAM | latest | https://github.com/centre-for-virus-research/weeSAM | sars-cov-2 |
| snipit | latest | https://github.com/aineniamh/snipit | sars-cov-2 |
| Trimmomatic-0.39 | 0.39 | https://github.com/usadellab/Trimmomatic/files/5854859/Trimmomatic-0.39.zip | BASH_scripting |
| Qualimap | latest | http://qualimap.conesalab.org/ | Coverage_plots |
| fastqc | latest | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | NGS_file_formats |
| tablet | latest | https://ics.hutton.ac.uk/tablet/download-tablet/ | NGS_file_formats Coverage_plots |
| IGV | latest | https://ics.hutton.ac.uk/tablet/download-tablet/ | NGS_file_formats Coverage_plots |
| SRA toolkit | latest | https://github.com/ncbi/sra-tools/wiki/ and https://github.com/ncbi/sra-tools/wiki/03.-Quick-Toolkit-Configuration | NGS_file_formats |
| Quast | latest | http://quast.sourceforge.net/quast.html | Coverage_plots |
| TempEst | latest | http://tree.bio.ed.ac.uk/software/tempest/ | Molecular Phylogeny |
| BEAST | latest | https://beast.community/install_on_unix | Molecular Phylogeny |
| BEAGLE | latest | https://beast.community/beagle | Molecular Phylogeny |
| Tracer | latest | https://github.com/beast-dev/tracer/releases/latest | Molecular Phylogeny |
| figtree | latest | : http://tree.bio.ed.ac.uk/software/figtree/ | Molecular Phylogeny |
| nano | latest | https://www.nano-editor.org/download.php | intro_to_linux |
| vim | latest | https://www.vim.org/download.php | intro_to_linux |
| Aliview | latest | https://ormbunkar.se/aliview/ | Multiple Sequence Alignment, Molecular Phylogeny |
| bcftools | latest | https://samtools.github.io/bcftools/bcftools.html | ngs/reference alignment/consensus |
| tablet | latest | https://ics.hutton.ac.uk/tablet/download-tablet/ | ngs/reference alignment/consensus |
| Lofreq | latest | https://csb5.github.io/lofreq/ | ngs/reference alignment/consensus |
| STAR | latest | https://github.com/alexdobin/STAR | ngs/reference alignment/consensus |
| HISAT2 | latest | http://daehwankimlab.github.io/hisat2/ | ngs/reference alignment/consensus |
| bwa | latest | http://bio-bwa.sourceforge.net/ | ngs/reference alignment/consensus |
| GATK | latest | https://gatk.broadinstitute.org/hc/en-us | ngs/reference alignment/consensus |
| PicardTools | latest | https://broadinstitute.github.io/picard/ | ngs/reference alignment/consensus |
| IGV | latest | https://software.broadinstitute.org/software/igv/ | ngs/reference alignment/consensus |
| VIVA | latest | https://github.com/compbiocore/VariantVisualization.jl | ngs/reference alignment/consensus |
| FastQC | latest | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | ngs/reference alignment/consensus |
| MultiQC | latest | multiqc.info | ngs/reference alignment/consensus |
| Samtools/htslib/bcftools | latest | http://samtools.sourceforge.net/ / http://www.htslib.org/ | ngs/reference alignment/consensus |
| trimgalore | latest | https://github.com/FelixKrueger/TrimGalore | ngs/reference alignment/consensus |
| prinseq | latest | http://prinseq.sourceforge.net/ | ngs/reference alignment/consensus |
| bam2fastq | latest | https://github.com/jts/bam2fastq | ngs/reference alignment/consensus |
| weesam | latest | https://bioinformatics.cvr.ac.uk/weesam-version-1-5/ | ngs/reference alignment/consensus |
| SameerReport | latest | (developed by Sreenu Vattipally) for generating mapping statistics. | ngs/reference alignment/consensus |
| example | example | example | example |
| PREVIOUS | VM | TOOLS | BELOW |
| Tempest | |||
| Figtree | |||
| Beast | v1.10.4 | ||
| fastqc | latest | ||
| spades | |||
| idba_ud | |||
| abyss | |||
| soap-denovo | |||
| garm | |||
| blastn | |||
| quast | |||
| scaffold-builder | |||
| mummer | |||
| diamond | |||
| Krona | |||
| centrifuge | https://ccb.jhu.edu/software/centrifuge/ | ||
| sra-toolkit | |||
| trim_galore | |||
| prinseq-lite | |||
| bwa | |||
| bowtie2 | |||
| minimap2 | |||
| samtools | |||
| bcftools | |||
| htslib | |||
| WeeSAM | |||
| tablet | https://ics.hutton.ac.uk/tablet/download-tablet/ | ||
| ivar | |||
| lofreq | |||
| SnpEff | |||
| VPhaser2 | |||
| VarScan2 | |||
| Java JDK | |||
| R | |||
| example | example | example | example |
| example | example | example | example |
NB: SARS-CoV-2 session - spear will ask if you want to install a pangolin env - options would be to selecte Yes (and not install pangolin separately) - or install pangolin first and then select No when installing spear. Also for ncov2019-artic-nf nextflow - I think the easiest will be to install via the conda route "-profile conda"
Diamond and Centrifuge - diamond db of viral proteins and the centrifuge db of bacteria, virus, archea and human.
krona and sra-toolkit - taxonomy and accession scripts for krona and sra-toolkit.
Genotyping servers (only online versions to be used)
Alignment-free approaches developed at Savitribai Phule Pune University
- Mumps virus: http://bioinfo.unipune.ac.in/Muv/Home.html
- Rhinoviruses: http://bioinfo.unipune.ac.in/RV-Typer/Home.html
- Dengue virus: http://bioinfo.unipune.ac.in/Dengue/Home.html
- West Nile virus: http://bioinfo.unipune.ac.in/WNV/Home.html
Alignment-based tools
- Genome Detective: https://www.genomedetective.com/app/typingtool/virus/