recipe pal_finder

Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them

Homepage:

http://sourceforge.net/projects/palfinder/

License:

GPLv3

Recipe:

/pal_finder/meta.yaml

Finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads, and designs PCR primers to amplify these repeat loci in an automated fashion. Exact matches to repeats or 2-, 3-, 4-, 5-, and/or 6-mers are located and primer3 is then used to generate primer pairs to amplify regions containing microsatellite loci.

package pal_finder

(downloads) docker_pal_finder

versions:

0.02.04-4,  0.02.04-3,  0.02.04-2,  0.02.04-1

depends perl:

depends primer3:

2.0.0a

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pal_finder

and update with::

   mamba update pal_finder

To create a new environment, run:

mamba create --name myenvname pal_finder

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pal_finder:<tag>

(see `pal_finder/tags`_ for valid values for ``<tag>``)

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Link to this page

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