cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads. (by COMBINE-lab)
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cuttlefish reviews and mentions

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  • Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    3 projects | /r/bioinformatics | 8 Sep 2022
    The paper describing a new tool from our lab has just been published in Genome Biology (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02743-6). Cuttlefish 2 is a tool for efficiently computing the compacted de Bruijn graph (or a spectrum preserving string set) from either raw sequencing reads or from reference genomes. It is quite fast and very memory efficient — for example, we were able to construct the compacted de Bruijn graph on a set of 661K bacterial genomes in 16 hours and 30 minutes using only 48.7GB of RAM. Construction of the compacted de Bruijn graph is an important initial processing step in e.g. genome assembly, and is also important in several other areas such as comparative genomics and as a critical step in building certain types of indices (e.g. [sshash](https://github.com/jermp/sshash)). You can find the cuttlefish 2 software on GitHub [here](https://github.com/COMBINE-lab/cuttlefish), and it can also be installed via Bioconda. We'd be happy to have your feedback!

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COMBINE-lab/cuttlefish is an open source project licensed under BSD 3-clause "New" or "Revised" License which is an OSI approved license.

The primary programming language of cuttlefish is C++.

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