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add conda in readme #10

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74abb9e
Update README.org
telatin Sep 27, 2023
107b9b7
fix syntax
telatin Sep 27, 2023
c864440
Update README.org
telatin Sep 27, 2023
98e39bb
Update README.org
telatin Sep 27, 2023
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25 changes: 19 additions & 6 deletions README.org
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Expand Up @@ -22,17 +22,30 @@ sequencing depth for consensus polishing - a common problem for a lot of rare
things from environmental metagenomic samples, for example.


** Usage
** Installation

Requires [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]] or newer for mapping.
Proovframe is available from
[[https://bioconda.github.io/recipes/proovframe/README.html][Bioconda]], and thus can
be installed with
[[https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/installing-with-conda.html][conda]],
which will also install its dependencies.

#+begin_src sh
conda install -c bioconda proovframe
#+end_src

If you decide to manual install the package cloning the repository,
consider that it requires [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]]
or newer (for mapping).

** Usage

#+begin_src sh
# install
git clone https://github.com/thackl/proovframe
# map proteins to reads
proovframe/bin/proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa
proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa

# fix frameshifts in reads
proovframe/bin/proovframe fix -o corrected-seqs.fa raw-seqs.fa raw-seqs.tsv
proovframe fix -o corrected-seqs.fa raw-seqs.fa raw-seqs.tsv
#+end_src

** Citing
Expand Down