1. Whats included in this installer ?

This installer includes addition/update of the following tools and hundreds of their dependencies;

  1. PathoScope2 - Species identification and strain attribution with unassembled sequencing data

  2. Prokka - Rapid prokaryotic genome annotation

  3. Roary - Rapid large-scale prokaryote pan genome analysis

  4. Snippy - Rapid bacterial SNP calling and core genome alignments

  5. MLST - Scan contig files against PubMLST typing schemes

  6. Abricate - Mass screening of contigs for antimicrobial and virulence genes

  7. Sixess - Rapid 16s rRNA identification from isolate FASTQ files

  8. SalmID - Rapid confirmation of Salmonella spp. and subspp. from sequence data

  9. MEGAN6 - a comprehensive toolbox for interactively analyzing microbiome data

  10. MetaPhlAn2 - profiling the composition of microbial communities from metagenomic sequencing data

  11. QIIME2 - a next-generation microbiome bioinformatics platform

  12. mothur - software to fill the bioinformatics needs of the microbial ecology community

  13. Krona Tools - Interactively explore metagenomes

  14. Staphopia-ap Staphopia analysis pipeline

  15. MASH - fast genome and metagenome distance estimation using MinHash

  16. QuickTree - reconstruction of phylogenies for very large protein families 

  17. MashTree - Create a tree using Mash distances

  18. Wgsim - a small tool for simulating sequence reads from a reference genome

  19. DAHAK - integrates state-of-the-art open source tools for metagenomic analyses

  20. vt - a variant tool set that discovers short variants from Next Generation Sequencing data

  21. MiniMap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences

  22. SNP-site - Rapidly extracts SNPs from a multi-FASTA alignment

  23. NGS tools - methods for population genetics analyses from NGS data

  24. SamTools 1.8 - a suite of programs for interacting with high-throughput sequencing data

  25. BcfTools 1.8 - a set of utilities that manipulate variant calls 

  26. Trimmomatic 0.38 - A flexible read trimming tool for Illumina NGS data

  27. tbl2asn - automates the creation of sequence records for submission to GenBank

  28. edirect - access to the NCBI’s suite of interconnected databases 

  29. Docker - open platform to build, ship, and run distributed applications

  30. Conda - Package, dependency and environment management for any language

2. Download Installer

Download the package installer from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=140

3. Prepare for install

3.1. Open a terminal. Move the ‘asm’ installer from your Dowonloads folder to your home folder using the below command (example screenshot below);

(You can also copy/paste the ‘asm’ installer from Downloads folder to the ‘ubuntu’ home folder, using the Desktop GUI interface, like you will do in a PC or MAC.

cp ~/Downloads/asm .

3.2. Make ‘asm’ installer executable, using the below command (example screenshot below)

chmod 755 asm


4. How to run the installer?

Run the script with the following command as example, in your working directory (example screenshot below).

ENTER THE DEFAULT parameters and ‘yes’ for any prompts in the middle of the install. The install should take about 10 minutes.

sudo ./asm


The setup assumes that you have not made any system level changes. If the install does not behave as expected, probably the system configuration has been changed. If you face any issues after this update, please let us know ASAP, so that we can help you troubleshoot the issue.

5. Issues ?

If you have any issues with running the installer or need any other information regarding this, please do not hesitate to contact us at contact at molbiocloud.com