Structural and functional analysis tools

Subsection Tool Galaxy wrapper
Name Version Subtools Name Revision
Search similarity NCBI BLAST [3][4] 2.2.30 Show database information ncbi_blast_plus 7f3c448e119b
Make BLAST database
Search protein database with protein query sequence(s)
Search translated nucleotide database with protein query sequence(s)
Make profile database
Search nucleotide database with nucleotide query sequence(s)
Mask low complexity regions
Search protein database with translated nucleotide query sequence(s)
Mask low-complexity regions in protein sequences
Search translated nucleotide database with translated nucleotide query sequence(s)
Search protein domain database (PSSMs) with protein query sequence(s)
Extract sequence(s) from BLAST database
Search protein domain database (PSSMs) with translated nucleotide query sequence(s)
Convert BLAST XML output to tabular
Convert masking information to file formats suitable for makeblastdb
Diamond <framework-tools-struct-funct-analysis-search-diamond> :cite:`buchfink_fast_2015 0.8.24 Build database from a FASTA file diamond df7738595640
Alignment tool for short sequences against a protein database
Map against reference genomes BWA [6][7][5] 0.7.12 Map with BWA-MEM (medium and long reads) bwa 546ada4a9f43
Map with BWA (short reads)
Assign taxonomy for 16S sequences Mothur [18] 1.36.1 More than 100 tools `suite_mothur <>`_  
Assign taxonomy for all sequence types MetaPhlAn2 [3] 2.5.0 Profile the composition of microbial communities metaphlan2 8991e05c44e4
Format MetaPhlAn2 output for Krona
Format MetaPhlAn2 output to extract abundance at different taxonomic levels 0.1.0   format_metaphlan2_output 2bfa9b200600
Kraken 0.10.5 Kraken suite_kraken_0_10_5 1bcf0e168661
Kraken’s confidence filter
Kraken report
Kraken translate
Analyze metabolism HUMAnN2 [1] 0.6.1 HUMAnN2 humann2 bcd414bb721b
Rename features of a HUMAnN2 generated table
Join HUMAnN2 generated tables
Reduce a HUMAnN2 generated table
Merge HUMAnN2 generated gene and pathway abundance tables
Renormalize a HUMAnN2 generated table
Regroup a HUMAnN2 generated table by features
Download HUMAnN2 databases
Group abundances of UniRef50 gene families obtained as HUMAnN2 output to Gene Ontology slim terms [2] 1.2.0   group_humann2_ uniref_abundances_to_go cad28d7b49d2
Compare outputs of HUMAnN2 for several samples and extract similar and specific information 0.1.0   compare_humann2_output c1aca37cb1fc
PICRUSt 1.0.1 Predict Metagenome suite_picrust 9f03d5b781fd
Categorize by function
Normalize OTUs by copy number
Combine functional and taxonomic results Combine MetaPhlAn2 and HUMAnN2 outputs 0.1.0   combine_metaphlan2_humann2 31394a0c0242

References

[1]Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. PLoS Comput Biol, 8(6):e1002358, June 2012. URL: http://dx.doi.org/10.1371/journal.pcbi.1002358, doi:10.1371/journal.pcbi.1002358.
[2]Bérénice Batut. Group abundances of UniRef50 gene families obtained with HUMAnN2 to Gene Ontology (GO) slim terms with relative abundances: release v1.2.0. 2016. URL: http://dx.doi.org/10.5281/zenodo.50086.
[3]Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L. Madden. BLAST+: architecture and applications. BMC Bioinformatics, 10(1):421, December 2009. URL: http://www.biomedcentral.com/1471-2105/10/421/abstract, doi:10.1186/1471-2105-10-421.
[4]Peter JA Cock, John M. Chilton, Björn Grüning, James E. Johnson, and Nicola Soranzo. NCBI BLAST+ integrated into Galaxy. GigaScience, 4(1):39, August 2015. URL: http://www.gigasciencejournal.com/content/4/1/39/abstract, doi:10.1186/s13742-015-0080-7.
[5]Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio], March 2013. arXiv: 1303.3997. URL: http://arxiv.org/abs/1303.3997.
[6]Heng Li and Richard Durbin. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14):1754–1760, July 2009. doi:10.1093/bioinformatics/btp324.
[7]Heng Li and Richard Durbin. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5):589–595, March 2010. URL: http://bioinformatics.oxfordjournals.org/content/26/5/589, doi:10.1093/bioinformatics/btp698.
[18]Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Horn, and Carolyn F. Weber. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl. Environ. Microbiol., 75(23):7537–7541, December 2009. URL: http://aem.asm.org/content/75/23/7537, doi:10.1128/AEM.01541-09.
[3]Duy Tin Truong, Eric A. Franzosa, Timothy L. Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Meth, 12(10):902–903, October 2015. URL: http://www.nature.com.gate1.inist.fr/nmeth/journal/v12/n10/full/nmeth.3589.html, doi:10.1038/nmeth.3589.