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Commit 2dd0566b authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion ♻️
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start changing simulation tool

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# Simulation # Simulation
[CAMISIM](https://github.com/CAMI-challenge/CAMISIM) can model different microbial abundance [InSilicoSeq](https://github.com/HadrienG/InSilicoSeq) is a sequencing simulator producing
profiles (from multi-sample time series to differential abundance studies) and was used to realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also
generate the benchmark data sets of the first CAMI challenge. be used to produce sequencing data from a single genome.
We describe here only the usage of de novo metagenomes simulation. For a more exhaustive We describe here only the usage for a simple simulation. For a more exhaustive documentation,
documentation, please refer to [CASISIM wiki](https://github.com/CAMI-challenge/CAMISIM/wiki). please refer to [InSilicoSeq documentation](https://insilicoseq.readthedocs.io/en/latest/?badge=latest).
## Install ## Install
CAMISIM contains a lot of dependencies and the list can be found [Here](https://github.com/CAMI-challenge/CAMISIM/wiki/User-manual#installation). You have several ways of installing InSilico seq that can be found [Here](https://insilicoseq.readthedocs.io/en/latest/iss/install.html).
However, we recommand the use of the docker image `cami/camisim:latest` or the singularity one ([here](https://gitlab.pasteur.fr/metagenomics/singularity/tree/master/tools/camisim), only from docker for the moment). Here, we will use of the docker image `hadrieng/insilicoseq:1.4.2` or the singularity one
([here]) built from the docker image.
## Run de novo metagenomes simulation ## Run de novo metagenomes simulation
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