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: 3.11.1
- 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
LRASM: Long Read Assembler
- Citation:
- Site: https://gitlab.com/chienchi/long_read_assembly
- Version: 0.1.0
- License: GPLv3
RACON
- Citation: Vaser R et al.(2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017 May;27(5):737-746.
- Site: https://github.com/isovic/racon
- Version: 1.3.1
- License: MIT

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: GPLv3
- 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: 1.13
- 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: 0.9
- 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: GPLv2
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: 25.6 (2018 Feb 27)
- License: Public Domain

Warning

tbl2asn must be compiled within the past year to function. We attempt to recompile every 6 months or so. Most recent compilation is 27 Feb 2018

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: 2.2.6
- 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: 2.23
- License: GPL
minimap2
- Citation: Li, H. (2017) Minimap2: fast pairwise alignment for long nucleotide sequences. arXiv:1708.01492
- Site: https://github.com/lh3/minimap2
- Version: 2.10
- License: MIT
diamond
- Citation: Buchfink, Xie C., D. Huson (2015) Fast and sensitive protein alignment using DIAMOND, Nature Methods 12, 59-60
- Site: https://github.com/bbuchfink/diamond
- Version: v0.9.22.123
- 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: 1.0
- 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/metaphlan2
- Version: 2.7.7
- 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
GOTTCHA2
- Citation:
- Site: https://gitlab.com/poeli/GOTTCHA2
- Version: 2.2.0
- License: BSD 3-Clause

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: 2.1.9
- 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

9.6. Specialty Genes¶

ShortBRED
- Citation: Kaminski J, et al. (2015) High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput Biol.18;11(12):e1004557.
- 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

9.7. 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: 2.7
- 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
bokeh
- Citation: Bokeh Development Team (2014). Bokeh: Python library for interactive visualization
- Site: https://bokeh.pydata.org/en/latest/
- Version: 0.12.10
- License: BSD 3-Clause

9.8. 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

R_3.3.2_Packages

Custom built direcotry containing all the packages required to install R packages offline

The majority of the packages were downloaded automatically using the following R commands.

# Function to get dependencies and imports for a given list of packages.
getPackages <- function(packs){
        packages <- unlist(
        tools::package_dependencies(packs, available.packages(), which=c("Depends", "Imports"), recursive=TRUE)
        )
packages <- union(packs, packages)
packages
}
# Use the function by providing the names of the desired packages.
packages <- getPackages(c("packageName", "packageName2"))
# For example
#packages <- getPackages(c("MetaComp","gtable","gridExtra","devtools","phyloseq","webshot","plotly","shiny","DT"))
# Download packages to current/desired directory.
download.packages(packages, destdir="./", type="source")
The packages specific to bioconductor needed to be manually downloade from the site
stringi defaults to downloading icudt55I.zip from online, the following method, from their documentation, was used to build a custom stringi package to avoid connecting to the internet.:
1. File the `git clone https://github.com/gagolews/stringi.git` command.
2. Edit the `.Rbuildignore` file and get rid of the `^src/icu55/data` line.
3. Run `R CMD build stringi_dir_name`.

MetaComp: EDGE Taxonomy Assignments Visualization
- Citation:
- Site: https://cran.r-project.org/
- Version: 1.0.2
- License: BSD 3-Clause
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: MIT/Expat 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://www.htslib.org/
- Version: 1.9
- 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: 2.08
- License: GPLv3
NanoPlot
- Citation: De Coster W, et al.(2018) NanoPack: visualizing and processing long read sequencing data, Bioinformatics. 2018 Mar 14.
- Site: https://github.com/wdecoster/NanoPlot
- Version: 1.13.0
- License: GPLv3
Porechop
- Citation:
- Site: https://github.com/rrwick/Porechop
- Version: 0.2.3
- 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: Free for academic, nonprofit, and personal use. A license is required for commercial usage.
sratoolkit
- Citation:
- Site: https://github.com/ncbi/sra-tools
- Version: 2.8.1
- License: Public Domain
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
Anaconda2Packages
- Custom built directory containing all the required python2 packages for offline installation.
- This was generated primarially using the command.:
```
pip download packageName
```
- Some packages were manually downloaded into the directory to install via conda
- Dependencies were manually downladed as they were discovered
Anaconda3 (Python 3)
- Citation:
- Site: https://anaconda.org
- Version: 5.1.0
- License: 3-clause BSD
Anaconda3Packages
- Custom built directory containing all the required python3 packages for offline installation.
- This was generated primarially using the command.:
```
pip download packageName
```

9.9. 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
DETEQT: Diagnostic targeted sequencing adjudication
- Citation:
- Site: https://github.com/LANL-Bioinformatics/DETEQT
- Version: 0.3.0
- License: GPLv3

9.10. RNA-Seq Analysis¶

PyPiReT: Pipeline for Reference based Transcriptomics.
- Citation:
- Site: https://github.com/mshakya/PyPiReT
- Version: 0.3.2
- License: GPLv3