9. Third Party Tools

9.1. 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: 3.5.0
  • License: GPLv2

9.2. 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:
  • Note: The original RATT program does not deal with reverse complement strain annotations transfer. We edited the source code to fix it.
• 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
  • Note: The NCBI tool tbl2asn included within PROKKA can have very slow runtimes (up to several hours) while it is dealing with numerous contigs, such as when we input metagenomic data. We modified the code to allow parallel processing using tbl2asn.
• 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: 2.2.29
  • 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
• tbl2asn
  • Citation:
  • Site: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
  • Version: 24.3 (2015 Apr 29th)
  • 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 26 Feb 2015

9.3. 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: 2.1.0
  • 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

9.4. 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: https://github.com/LANL-Bioinformatics/GOTTCHA
  • Version: 1.0b
  • License: GPLv3

9.5. 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

9.6. Visualization and Graphic User Interface

• JQuery Mobile
  • Site: http://jquerymobile.com
  • Version :1.4.3
  • License: CC0
• 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: 2.4
  • License: BSD

9.7. 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: 2.15.3
  • 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: 2.4.4
  • License: