8. Third Party Tools

8.1. Assembly

• IDBA-UD
  • Citation: Peng, Y., et al. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420-1428.
  • Site: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
  • Version: 1.1.1
  • License: GPLv2
• SPAdes
  • Citation: Nurk, Bankevich et al. (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013 Oct;20(10):714-37
  • Site: http://bioinf.spbau.ru/spades
  • Version: 3.7.1
  • License: GPLv2
• MEGAHIT
  • Citation: Li D. et al. (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015 May 15;31(10):1674-6
  • Site: https://github.com/voutcn/megahit
  • Version: 1.0.3
  • License: GPLv3

8.2. Annotation

• RATT
  • Citation: Otto, T.D., et al. (2011) RATT: Rapid Annotation Transfer Tool, Nucleic acids research, 39, e57.
  • Site: http://ratt.sourceforge.net/
  • Version:
  • License:
• Prokka
  • Citation: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30,2068-2069.
  • Site: http://www.vicbioinformatics.com/software.prokka.shtml
  • Version: 1.11
  • License: GPLv2
• tRNAscan
  • Citation: Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic acids research, 25, 955-964.
  • Site: http://lowelab.ucsc.edu/tRNAscan-SE/
  • Version: 1.3.1
  • License: GPLv2
• Barrnap
  • Citation:
  • Site: http://www.vicbioinformatics.com/software.barrnap.shtml
  • Version: 0.42
  • License: GPLv3
• BLAST+
  • Citation: Camacho, C., et al. (2009) BLAST+: architecture and applications, BMC bioinformatics, 10, 421.
  • Site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/
  • Version: 2.5.0
  • License: Public domain
• blastall
  • Citation: Altschul, S.F., et al. (1990) Basic local alignment search tool, Journal of molecular biology, 215, 403-410.
  • Site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/
  • Version: 2.2.26
  • License: Public domain
• Phage_Finder
  • Citation: Fouts, D.E. (2006) Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic acids research, 34, 5839-5851.
  • Site: http://phage-finder.sourceforge.net/
  • Version: 2.1
  • License: GPLv3
• Glimmer
  • Citation: Delcher, A.L., et al. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics, 23, 673-679.
  • Site: http://ccb.jhu.edu/software/glimmer/index.shtml
  • Version: 302b
  • License: Artistic License
• ARAGORN
  • Citation: Laslett, D. and Canback, B. (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences, Nucleic acids research, 32, 11-16.
  • Site: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
  • Version: 1.2.36
  • License:
• Prodigal
  • Citation: Hyatt, D., et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC bioinformatics, 11, 119.
  • Site: http://prodigal.ornl.gov/
  • Version: 2_60
  • License: GPLv3
• ShortBRED
  • Citation: Kaminski J et al. (2015) High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PLoS Comput Biol. 2015 Dec 18;11(12):e1004557
  • Site: http://huttenhower.sph.harvard.edu/shortbred
  • Version: 0.9.4
  • License:
• tbl2asn
  • Citation:
  • Site: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
  • Version: 24.9 (2016 Feb 3rd)
  • License:

Warning

tbl2asn must be compiled within the past year to function. We attempt to recompile every 6 months or so. Most recent compilation is 3 Feb 2016

8.3. Alignment

• HMMER3
  • Citation: Eddy, S.R. (2011) Accelerated Profile HMM Searches, PLoS computational biology, 7, e1002195
  • Site: http://hmmer.janelia.org/
  • Version: 3.1b1
  • License: GPLv3
• Infernal
  • Citation: Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, 29, 2933-2935.
  • Site: http://infernal.janelia.org/
  • Version: 1.1rc4
  • License: GPLv3
• Bowtie 2
  • Citation: Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2, Nature methods, 9, 357-359.
  • Site: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
  • Version: 2.2.6
  • License: GPLv3
• BWA
  • Citation: Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754-1760.
  • Site: http://bio-bwa.sourceforge.net/
  • Version: 0.7.12
  • License: GPLv3
• MUMmer3
  • Citation: Kurtz, S., et al. (2004) Versatile and open software for comparing large genomes, Genome biology, 5, R12.
  • Site: http://mummer.sourceforge.net/
  • Version: 3.23
  • License: GPLv3
• RAPSearch2
  • Citation: Zhao et al. (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012 Jan 1;28(1):125-6
  • Site: http://omics.informatics.indiana.edu/mg/RAPSearch2/
  • Version: 2.22
  • License: GPL

8.4. Taxonomy Classification

• Kraken
  • Citation: Wood, D.E. and Salzberg, S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome biology, 15, R46.
  • Site: http://ccb.jhu.edu/software/kraken/
  • Version: 0.10.4-beta
  • License: GPLv3
• Metaphlan
  • Citation: Segata, N., et al. (2012) Metagenomic microbial community profiling using unique clade-specific marker genes, Nature methods, 9, 811-814.
  • Site: http://huttenhower.sph.harvard.edu/metaphlan
  • Version: 1.7.7
  • License: Artistic License
• GOTTCHA
  • Citation: Tracey Allen K. Freitas, Po-E Li, Matthew B. Scholz, Patrick S. G. Chain (2015) Accurate Metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Research (DOI: 10.1093/nar/gkv180)
  • Site: http://lanl-bioinformatics.github.io/GOTTCHA/
  • Version: 1.0b
  • License: GPLv3

8.5. Phylogeny

• FastTree
  • Citation: Morgan N. Price, Paramvir S. Dehal, and Adam P. Arkin. 2009. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Mol Biol Evol (2009) 26 (7): 1641-1650
  • Site: http://www.microbesonline.org/fasttree/
  • Version: 2.1.7
  • License: GPLv2
• RAxML
  • Citation: Stamatakis,A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30:1312-1313
  • Site: http://sco.h-its.org/exelixis/web/software/raxml/index.html
  • Version: 8.0.26
  • License: GPLv2
• Bio::Phylo
  • Citation: Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, (2011). Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63.
  • Site: http://search.cpan.org/~rvosa/Bio-Phylo/
  • Version: 0.58
  • License: GPLv3
• PhaME
  • Citation: Sanaa Afroz Ahmed, Chien-Chi Lo, Po-E Li, Karen W Davenport, Patrick S.G. Chain. From raw reads to trees: Whole genome SNP phylogenetics across the tree of life. bioRxiv doi: http://dx.doi.org/10.1101/032250
  • Site: https://github.com/LANL-Bioinformatics/PhaME/
  • Version: 1.0
  • License: GPLv3

8.6. Specialty Genes

• ShortBRED
  • Citation: James Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam Dantas, and Curtis Huttenhower. Fast and Accurate Metagenomic Search with ShortBRED.
  • Site: `https://huttenhower.sph.harvard.edu/shortbred`_
  • Version: 0.9.4M
  • License: MIT
• RGI (Resistance Gene Identifier)
  • Citation: McArthur & Wright. 2015. Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. Current Opinion in Microbiology, 27, 45-50.
  • Site: `https://card.mcmaster.ca/analyze/rgi`_
  • Version: 3.1.1
  • License: Apache Software License

8.7. Visualization and Graphic User Interface

• jsPhyloSVG
  • Citation: Smits SA, Ouverney CC, (2010) jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web. PLoS ONE 5(8): e12267.
  • Site: http://www.jsphylosvg.com
  • Version: 1.55
  • License: GPL
• JBrowse
  • Citation: Skinner, M.E., et al. (2009) JBrowse: a next-generation genome browser, Genome research, 19, 1630-1638.
  • Site: http://jbrowse.org
  • Version: 1.11.6
  • License: Artistic License 2.0/LGPLv.1
• KronaTools
  • Citation: Ondov, B.D., Bergman, N.H. and Phillippy, A.M. (2011) Interactive metagenomic visualization in a Web browser, BMC bioinformatics, 12, 385.
  • Site: http://sourceforge.net/projects/krona/
  • Version: 2.6
  • License: BSD
• JQuery
  • Site: http://jquery.com/
  • Version: 1.10.2
  • License: MIT
• JQuery Mobile
  • Site: http://jquerymobile.com
  • Version: 1.4.3
  • License: CC0
• DataTables
  • Site: https://datatables.net
  • Version: 1.10.11
  • License: MIT
• jQuery File Tree
  • Site: http://www.abeautifulsite.net/jquery-file-tree/
  • Version: 1.01
  • License: GPL and MIT
• Raphael - JavaScript Vector Library
  • Site: http://dmitrybaranovskiy.github.io/raphael/
  • Version: 1.4.3
  • License: MIT
• Tooltipster
  • Site: http://iamceege.github.io/tooltipster/
  • Version: 3.2.6
  • License: MIT
• Lazy Load XT
  • Site: http://ressio.github.io/lazy-load-xt/
  • Version: 1.0.6
  • License: MIT
• Plupload
  • Site: http://www.plupload.com
  • Version: 2.1.7
  • License: GPLv2 and OEM
• hello.js
  • Site: http://adodson.com/hello.js/
  • Version: 1.8.1
  • License: MIT

8.8. Utility

• BEDTools
  • Citation: Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841-842.
  • Site: https://github.com/arq5x/bedtools2
  • Version: 2.19.1
  • License: GPLv2
• R
  • Citation: R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
  • Site: http://www.r-project.org/
  • Version: 3.3.2
  • License: GPLv2
• GNU_parallel
  • Citation: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47
  • Site: http://www.gnu.org/software/parallel/
  • Version: 20140622
  • License: GPLv3
• tabix
  • Citation:
  • Site: http://sourceforge.net/projects/samtools/files/tabix/
  • Version: 0.2.6
  • License:
• Primer3
  • Citation: Untergasser, A., et al. (2012) Primer3–new capabilities and interfaces, Nucleic acids research, 40, e115.
  • Site: http://primer3.sourceforge.net/
  • Version: 2.3.5
  • License: GPLv2
• SAMtools
  • Citation: Li, H., et al. (2009) The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078-2079.
  • Site: http://samtools.sourceforge.net/
  • Version: 0.1.19
  • License: MIT

• FaQCs
  • Citation: Chienchi Lo, PatrickS.G. Chain (2014) Rapid evaluation and Quality Control of Next Generation Sequencing Data with FaQCs. BMC Bioinformatics. 2014 Nov 19;15
  • Site: https://github.com/LANL-Bioinformatics/FaQCs
  • Version: 1.34
  • License: GPLv3
• wigToBigWig
  • Citation: Kent, W.J., et al. (2010) BigWig and BigBed: enabling browsing of large distributed datasets, Bioinformatics, 26, 2204-2207.
  • Site: https://genome.ucsc.edu/goldenPath/help/bigWig.html#Ex3
  • Version: 4
  • License:
• sratoolkit
  • Citation:
  • Site: https://github.com/ncbi/sra-tools
  • Version: 2.5.4
  • License:
• ea-utils
  • Citation: Erik Aronesty (2011) ea-utils : “Command-line tools for processing biological sequencing data”
  • Site: https://code.google.com/archive/p/ea-utils/
  • Version: 1.1.2-537
  • License: MIT License
• Anaconda2 (Python 2)
  • Citation:
  • Site: `https://anaconda.org`_
  • Version: 4.1.1
  • License: 3-clause BSD

8.9. Amplicon Analysis

• QIIME
  • Citation: Caporaso et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May;7(5):335-6
  • Site: http://qiime.org/
  • Version: 1.9.1
  • License: GPLv2