recipe sprai

Sprai (single-pass read accuracy improver) is a tool to correct sequencing errors in single-pass reads for de novo assembly. It is originally designed for correcting sequencing errors in single-molecule DNA sequencing reads, especially in Continuous Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is not maximizing the accuracy of error-corrected reads; instead, Sprai aims at maximizing the continuity (i.e., N50 contig length) of assembled contigs after error correction.

Homepage:

http://zombie.cb.k.u-tokyo.ac.jp/sprai/

License:

MIT License

Recipe:

/sprai/meta.yaml

package sprai

versions:

0.9.9.23-0

depends blast:

depends libgcc:

depends perl:

5.22.0*

depends perl-app-cpanminus:

depends perl-module-build:

depends python:

2.7*

depends wgs-assembler:

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 sprai

and update with::

   mamba update sprai

To create a new environment, run:

mamba create --name myenvname sprai

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/sprai:<tag>

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

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