Resources: Galaxy tools

Select a tag (or keyword) from the list below to browse through available resources in that category.

Tag

Resources

Info

  • Select a resource to see details.

View more ›

Top Rated

The following are top-rated resources of this type.

  1. STACKS populations: Run the STACKS populations program

    14 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program, part of the STACKS pipeline, will be executed in place of the genotypes program when a population is being processed through the pipeline. A map specifiying which individuals belong to which population is submitted to the …

  2. STACKS Process Radtags: Run the STACKS cleaning script

    14 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance …

  3. Map with BWA for STACKS: from zip file with fastqsanger files

    14 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The original resource is available here BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short …

  4. STACKS Reference map: Run the STACKS ref_map.pl wrapper

    15 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. This program will execute each of the Stacks components: first, running …

  5. STACKS assemble read pairs by locus: Run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers

    15 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results.

  6. STACKS genotypes: Run the STACKS genotypes program

    15 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program exports a Stacks data set either as a set of observed haplotypes at each locus in the population, or with the haplotypes encoded into genotypes. The -r option allows only loci that exist in a certain number of population …

  7. STACKS Prepare population map file for STACKS denovomap and refmap

    15 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This tools allow users to generate a population map for denovo map or reference map STACKS pipeline from a STACKS Process radtags output archive and a tab delimited file with population informations.

  8. STACKS De novo map: Run the STACKS denovo_map.pl wrapper

    15 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as …

  9. COMMET: COmpare Multiple METagenomes

    17 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. Directly from non-assembled reads, all against all comparisons are performed through an efficient …

  10. USEARCH search for one (default) or a few high-identity hits to a database

    17 Sep 2014 | Galaxy tools | Contributor(s): Yvan Le Bras, Cyril Monjeaud

    The tool is available in the GenOuest Galaxy instance here Searches for one (default) or a few high-identity hits to a database using global alignment. The id option is required; this specifies the minimum identity for a hit. To get more than one hit, increase -maxaccepts (see …