recipe hifiadapterfilt

Convert .bam to .fastq and remove reads with remnant PacBio HiFi adapter sequences

Homepage:

https://bio.tools/hifiadapterfilt

Developer docs:

https://github.com/sheinasim/HiFiAdapterFilt

License:

GPL3 / GPL-3.0-or-later

Recipe:

/hifiadapterfilt/meta.yaml

Links:

biotools: hifiadapterfilt, doi: 10.1186/s12864-022-08375-1

package hifiadapterfilt

(downloads) docker_hifiadapterfilt

versions:

3.0.0-0

depends bamtools:

depends blast:

depends ncbi-fcs-gx:

depends pigz:

requirements:

additional platforms:

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 hifiadapterfilt

and update with::

   mamba update hifiadapterfilt

To create a new environment, run:

mamba create --name myenvname hifiadapterfilt

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/hifiadapterfilt:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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