Metavisitor subdomain

index-metavisitor.md

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+---
+layout: subsite-galaxy
+website: https://metavisitor.usegalaxy.eu
+subdomain: metavisitor
+gitter: ARTbio/metavisitor
+---
+
+# Welcome to the Metavisitor Galaxy instance
+
+<img src="/assets/media/Galaxy-metavisitor-logo.png" alt="Galaxy Metavisitor"/>
+
+{:.no_toc}
+
+[Metavisitor](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168397) is
+a user-friendly and adaptable software to provide biologists, clinical researchers
+and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral
+genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows
+was implemented as the Metavisitor package in the [Galaxy framework](https://galaxyproject.org){:target="_blank"}.
+Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing
+Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules.
+
+The Metavisitor Galaxy implementation comprises tools and workflows that are maintained in
+[ARTbio/metavisitor GitHub repository](https://github.com/ARTbio/metavisitor/tree/metavisitor2/extra-files/metavisitor)
+
+# Content
+{:.no_toc}
+
+1. TOC
+{:toc}
+
+
+# Get started
+
+Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface.
+
+# Training
+
+**Want to learn more about Galaxy? Check out the following hands-on tutorials from [the Galaxy Training Network](https://galaxyproject.github.io/training-material/){:target=_"blank"}.**
+
+
+# Available tools
+
+Tool | Description | Reference
+--- | --- | ---
+{% include tool.html id="blast_to_scaffold" %} | blast_to_scaffold - Generate DNA scaffold from blastn or tblastx alignment of Contigs  | -
+{% include tool.html id="bowtie2" %} | Bowtie2 - map reads against reference genome | -
+{% include tool.html id="cherry_pick_fasta" %} | Pick Fasta sequences - with header satisfying a query string | -
+{% include tool.html id="concatenate_multiple_datasets" %} | Concatenate multiple datasets - tail-to-head by specifying how | -
+{% include tool.html id="data_manager_bowtie2_index_builder" %} | Bowtie2 index - Data Manager for building bowtie2 indexes | -
+{% include tool.html id="data_manager_bowtie_index_builder" %} | Bowtie index - Data Manager for building bowtie indexes | -
+{% include tool.html id="data_manager_fetch_genome_dbkeys_all_fasta" %} | Create DBKey and Reference Genome - Allows optionally defining a new DBKEY and retrieves a FASTA file and populate the all_fasta.loc data table | -
+{% include tool.html id="fasta_filter_by_length" %} | Filter sequences by length | -
+{% include tool.html id="fastx_trimmer" %} | Trim sequences | -
+{% include tool.html id="fetch_fasta_from_ncbi" %} | Retrieve FASTA from NCBI | -
+{% include tool.html id="khmer_normalize_by_median" %} | Normalize By Median - Filter reads using digital normalization via k-mer abundances | -
+{% include tool.html id="blastparser_and_hits" %} | Parse blast output and compile hits - for virus discovery | -
+{% include tool.html id="cap3" %} | cap3 - Sequence Assembly tool | -
+{% include tool.html id="sequence_format_converter" %} | sequence_format_converter - various fasta to tabular conversions | -
+{% include tool.html id="oases" %} | Oases_optimiser - Auto optimise de novo RNA-seq Oases/Velvet assembly | -
+{% include tool.html id="sr_bowtie" %} | sR_bowtie - for small RNA short reads | -
+{% include tool.html id="small_rna_maps" %} | small_rna_maps - Generates small read maps from alignment BAM files | -
+{% include tool.html id="ncbi_blast_plus" %} | ncbi_blast_plus - NCBI BLAST+ | -
+{% include tool.html id="regex_find_replace" %} | Regex Find And Replace - Use python regular expressions to find and replace text | -
+{% include tool.html id="sra_tools" %} | sra_tools - NCBI Sequence Read Archive toolkit utilities | -
+{% include tool.html id="trinity" %} | trinity - Trinity (from the Trinity tool suite) | -
+{% include tool.html id="spades" %} | spades - St. Petersburg genome assembler | -
+{% include tool.html id="yac_clipper" %} | yac_clipper - Clips 3' adapters for small RNA sequencing reads | -
+{% include tool.html id="vsearch" %} | VSearch search - VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences | -
+{% include tool.html id="blast_unmatched" %} | Blast Unmatched - get query sequences that didn't get a match during a blast | -
+{% include tool.html id="fasta_compute_length" %} | fasta_compute_length - Compute sequence length | -
+{: .table.table-striped .tooltable}
+
+
+# Acknowledgments
+
+The authors would like to thank Björn Grüning and @galaxyproject
+
+# Citation
+
+Please add the following when using the [metavisitor.usegalaxy.eu](https://metavisitor.usegalaxy.eu) Galaxy portal:
+
+*The Galaxy server that was used for some calculations is in part funded by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012) and
+German Federal Ministry of Education and Research (BMBF grants 031 A538A/A538C RBC, 031L0101B/031L0101C de.NBI-epi, 031L0106 de.STAIR (de.NBI)).*
+
+More information on [how to cite Galaxy](https://galaxyproject.org/citing-galaxy/).