MiGA Manual
AboutCodebaseMiGA Online
Primary version
Primary version
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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On this page
  • Enveomics Collection
  • NCBI BLAST+
  • HMMer 3
  • SolexaQA++
  • Scythe
  • FastQC
  • IDBA-UD
  • Prodigal
  • Barrnap
  • Bedtools
  • MyTaxa
  • Krona
  • MCL
  • Ape
  • Vegan
  • Diamond
  • FastANI
  1. Part V: Additional details

External Software

PreviousMetadataNextPart VI: Workflows

Last updated 5 years ago

Enveomics Collection

Rodriguez-R LM, and Konstantinidis KT (2016). The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. .

NCBI BLAST+

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, and Madden TL (2009). BLAST+: architecture and applications. .

HMMer 3

Mistry J, Finn RD, Eddy SR, Bateman A, and Punta M (2013). Challenges in Homology Search: HMMER3 and Convergent Evolution of Coiled-Coil Regions. .

SolexaQA++

Cox MP, Peterson DA, and Biggs PJ (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. .

Scythe

, by Vince Buffalo.

FastQC

IDBA-UD

Prodigal

Barrnap

Bedtools

MyTaxa

Krona

MCL

Ape

Vegan

Diamond

FastANI

, by Simon Andrews.

Peng Y. Leung HC, Yiu SM, and Chin FY (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. .

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. .

, by Torsten Seemann.

, by the Quinlan Laboratory.

Luo C, Rodriguez-R LM, and Konstantinidis KT (2014). MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. .

Ondov BD, Bergman NH, and Phillippy AM (2011). Interactive metagenomic visualization in a Web browser. .

Enright AJ, Van Dongen S, and Ouzounis CA (2002). An efficient algorithm for large-scale detection of protein families. .

Paradis E, Claude J, and Strimmer K (2004). APE: Analyses of Phylogenetics and Evolution in R language. .

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHM, Szoecs E, and Wagner H (2017). Vegan: Community Ecology Package. .

Buchfink B, XieC, and Huson DH (2015). Fast and Sensitive Protein Alignment using DIAMOND. .

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, and Aluru S (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. .

PeerJ Preprints 4:e1900v1
BMC Bioinformatics 10:421
Nucleic Acids Res 41:e121
BMC Bioinformatics 11:485
GitHub: vsbuffalo/scythe
FastQC site
Bioinformatics, 28:1420-1428
BMC Bioinformatics, 11(1):119
GitHub: tseemann/barrnap
Bedtools site
Nucleic Acids Res, 42(8):e73
BMC Bioinformatics 12:385
Nucleic Acids Res 30(7):1575-1584
Bioinformatics 20(2):289-290
R package
Nature Methods 12:59–60
Nature Comm 9:5114