MeDuSa 1.6 – Multi-draft based Scaffolder

MeDuSa 1.6

:: DESCRIPTION

MeDuSa (Multi-Draft based Scaffolder) is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

::DEVELOPER

Florence Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Java

:: DOWNLOAD

  MeDuSa

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 25. pii: btv171.
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M

eggNOG-mapper 2.0.1 – Fast Genome-wide Functional Annotation through Orthology Assignment

eggNOG-mapper 2.0.1

:: DESCRIPTION

eggNOG-mapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

eggNOG-mapper

:: MORE INFORMATION

Citation

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering & Peer Bork.
Mol Biol Evol (2017) doi: 10.1093/molbev/msx148.

SmashCommunity 1.6p2 – Metagenomic Analysis and Annotation Tool

SmashCommunity 1.6p2

:: DESCRIPTION

 SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SmashCommunity

:: MORE INFORMATION

Citation

Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J. and P. Bork. (2010)
SmashCommunity: A metagenomic annotation and analysis tool,
Bioinformatics, 26, 2977-8.

 

Sircah 1.0 – Detection and Visualization of Alternative Transcripts

Sircah 1.0

:: DESCRIPTION

Sircah is an application written in python that dectects and visualises alternative splicing events using spliced alignments.Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription. Such transcript models may come from the gene prediction pipelines of genome databases or from spliced alignments of ESTs or proteins against the genome.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Sircah

:: MORE INFORMATION

Citation

Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington ED, Bork P.
Bioinformatics. 2008 Sep 1;24(17):1959-60. Epub 2008 Jul 17.

 

MOCAT2 2.0 – Analyzing Metagenomics Datasets

MOCAT2 2.0

:: DESCRIPTION

MOCAT (Metagenomics Analysis Toolkit) is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format. Using MOCAT you can, for example, generate taxonomic profiles of, and assemble, metagenomes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MOCAT

:: MORE INFORMATION

Citation:

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.
Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183.

PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17.
MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P.

specI 1.0 – Species Identification tool

specI 1.0

:: DESCRIPTION

specI is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Perl
  • usearch
  • glsearch

:: DOWNLOAD

 specI

:: MORE INFORMATION

Citation

Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28.
Accurate and universal delineation of prokaryotic species.
Mende DR1, Sunagawa S, Zeller G, Bork P.

jMOTU 1.0.7 / Taxonerator 0.9 – Analysis of Large DNA Barcode Datasets

jMOTU 1.0.7 / Taxonerator 0.9

:: DESCRIPTION

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU).

Taxonnerator is a software package for carrying out simple similarity-based annotation of clustered barcode sequence data produced by jMOTU. It generates taxonomic annotation for MOTU by BLASTing representative sequences against a preformatted database of sequences from known organisms (available from this website). Taxonnerator is useful for initial taxonomic investigation of environmental barcode datasets. For each database sequence showing significant similarity to a MOTU, taxonomic information is stored at all taxonomic levels.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

jMOTUTaxonerator

:: MORE INFORMATION

Citation

PLoS One. 2011 Apr 25;6(4):e19259. doi: 10.1371/journal.pone.0019259.
jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.
Jones M1, Ghoorah A, Blaxter M.

BLAST2GENE – Gene Analysis in Genomic Regions

BLAST2GENE

:: DESCRIPTION

BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 BLAST2GENE

:: MORE INFORMATION

Citation

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama M, Torrents D, Bork P
Bioinformatics. 2004 Aug 12; 20(12): 1968-70. Epub 2004 Mar 22; PubMed: 15037510.

Platypus Conquistador 0.9.0 – Confirming Specific Taxonomic Groups within your Samples

Platypus Conquistador 0.9.0

:: DESCRIPTION

Platypus Conquistador is a bioinformatic command line tool for the confirmation of the presence/absence of a specific taxon (or set of taxa) in environmental shotgun sequence reads.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Platypus Conquistador

:: MORE INFORMATION

BOND – Basic OligoNucleotide Design

BOND

:: DESCRIPTION

BOND is a program for designing DNA oligonucleotides. In comprehensive testing, it achieved 100% sensitivity and specificity.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BOND

:: MORE INFORMATION

Citation

BOND: Basic OligoNucleotide Design.
Ilie L, Mohamadi H, Golding GB, Smyth WF.
BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.