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Update README
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martin-steinegger authored Apr 1, 2019
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Expand Up @@ -138,17 +138,23 @@ MMseqs2 provides many additional search modes:
* Very fast and sensitive Searches against [profile databases such as the PFAM](https://github.com/soedinglab/MMseqs2/wiki#how-to-create-a-target-profile-database-from-pfam)
* [Reciprocal best hits search](https://github.com/soedinglab/MMseqs2/wiki#reciprocal-best-hit-using-mmseqs-rbh)


Many modes can also be combined. You can, for example, do a translated nucleotide against protein profile search.

## How to cluster
Before clustering, convert your database into the MMseqs2 database format:

mmseqs createdb examples/DB.fasta DB

Then execute the clustering:
Adjust the [clustering criteria](htt ps://github.com/soedinglab/MMseqs2/wiki#clustering-criteria) and then execute the cluster workflow (more senstivie)

mmseqs cluster DB clu tmp

or linclust (faster less sensitive):

mmseqs linclust DB clu tmp


Please ensure that in case of large input databases the temporary direcotry provides enough free space.
For disk space requirements, see the user guide.

Expand All @@ -166,7 +172,7 @@ To extract the representative sequences from the clustering result call:
mmseqs result2repseq DB clu DB_clu_rep
mmseqs result2flat DB DB DB_clu_rep DB_clu_rep.fasta --use-fasta-header

Read more about the format [here](https://github.com/soedinglab/mmseqs2/wiki#clustering-format).
Read more about the format [here](https://github.com/soedinglab/mmseqs2/wiki#clustering-format)

### Memory Requirements
MMseqs2 checks the available memory of the computer and automatically divide the target database in parts that fit into memory. Splitting the database will increase the runtime slightly.
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