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Update README with usage and DIAMOND requirements #12

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13 changes: 12 additions & 1 deletion README.org
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Expand Up @@ -24,13 +24,24 @@ things from environmental metagenomic samples, for example.

** Usage

Requires [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]] or newer for mapping.
Proovframe internally uses a diamond db containing protein sequences to map against.
This can either be generated or provided as input.
Therefore, proovframe requires [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]]
or newer for mapping.

#+begin_src sh
# install
git clone https://github.com/thackl/proovframe

## first step: map
# map proteins to reads
proovframe/bin/proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa
# select the diamond mode for db generation
proovframe/bin/proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa --diamond-mode [fast,sensitive,{mid,more,very,ultra}-sensitive]
# map against a pre-computed protein db
proovframe/bin/proovframe map --db diamond.dmnd -o raw-seqs.tsv raw-seqs.fa

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