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common_progs.md

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Common Bioinformatics Software

  • StaPH-B – State public health bioinformaticians workgroup

  • ABiL(Applied Bioinformatics Laboratory) – a partnership between Georgia Tech and IHRC, Inc to provide bioinformatic training and resources

  • Abricate – program that screens the assembled contigs for virulence genes and acquired resistance genes

  • Apache Guacamole – application that allows for remote desktop access

  • BaseSpace – user friendly workspace to manage, analyze and share sequencing data from Illumina machines

  • BLAST – Basic Local Alignment Search Tool, used to identify regions of similarity between amino acid or nucleotide sequences against a database or a known sequence that are above a specific threshold

  • CLC Genomics Workbench – user friendly workspace for bioinformatics analysis and visualization of sequencing data, can also be used for metagenomics and RNA-seq analysis and will support sequencing data from Illumina, IonTorrent, PacBio, and GeneReader sequencing machines

  • FastQC – program that is used for quality control of raw reads

  • Galaxy – web based platform for data analysis, this platform is used by Genome Trakr for sequencing analysis

  • Illumina – company that provides the technology for sequencing and analysis of genomics and molecular diagnostics

  • IqTree – program used for phylogenetic inference using maximum likelihood with fast bootstrapping and ability to change the model used for analysis

  • Kraken – taxonomic sequence classifier program that examines k-mers within a read and queries a database with those k-mers. This database contains a mapping of every k-mer in Kraken genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain k-mer.

  • Lyve – SET – (SET: Snp Extraction Tool) core genome pipeline using RaXML to examine relatedness of strains for outbreak investigation, hqSNP (high quality SNP analysis)

  • Mash – distance estimate for genome and metagenomes

  • Microbe TRACE (TRAnsmission Cluster Engine) – A tool for the large-scale Molecular Epidemiology of Microbial diseases and a platform for viewing and comparing genomic and contact tracing networks by the CDC. It generates network diagrams of clusters based on genetic distance data.

  • PROKKA – rapid prokaryotic genome annotation

  • Quast – evaluates the quality of the assembled genome

  • Raspberry Pi – a small computing chip (size of a credit card) that can be plugged into any monitor (TV or computer) and can be used to learn basic programming using Python or Scratch, commonly used in K-12 STEM education to teach computer science

  • Roary – identifies the pan genome using annotated assemblies from Prokka, utilized for reference free phylogenetic analysis

  • Seq Sero – Salmonella serotype identification for more than 2,300 serotypes from raw sequencing reads and genome assemblies

  • Serotype finder - serotyping of Escherichia coli

  • Shovill – faster Spades assembler, can also run other assemblers (ie Velvet)

  • SISTR – Salmonella in silico typing resource, alternative to SeqSero

  • Spades – utilized for the de novo assembly of raw reads into contigs

  • Trimmomatic – read and adapter trimming of the raw reads

  • Unicycler – assembly pipeline that can assemble short read and long read only sets as well as hybrid sets that combine short and long reads

  • Velvet – package that was developed for sequencing assembly of short reads