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        "description": "# InSilicoSeq\n\n## A sequencing simulator\n\n[![Build Status](https://github.com/HadrienG/InsilicoSeq/workflows/CI/badge.svg)](https://github.com/HadrienG/InSilicoSeq/actions)\n[![Documentation Status](https://readthedocs.org/projects/insilicoseq/badge/?version=latest)](http://insilicoseq.readthedocs.io/en/latest/?badge=latest)\n[![PyPI version](https://badge.fury.io/py/InSilicoSeq.svg)](https://badge.fury.io/py/InSilicoSeq)\n[![codecov](https://codecov.io/gh/HadrienG/InSilicoSeq/branch/master/graph/badge.svg)](https://codecov.io/gh/HadrienG/InSilicoSeq)\n[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty630-blue.svg)](https://doi.org/10.1093/bioinformatics/bty630)\n[![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](LICENSE)\n\nInSilicoSeq is a sequencing simulator producing realistic Illumina reads.\nPrimarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.\n\nInSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.\n\nInSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided.\n\n## Installation\n\nInsilicoseq is Available in [bioconda](https://bioconda.github.io/).\n\nTo install with conda:\n\n```shell\nconda install -c bioconda insilicoseq\n```\n\nOr with pip:\n\n```shell\npip install InSilicoSeq\n```\n\n_Note:_ Insilicoseq requires python >= 3.5 \n\nAlternatively, with docker:\n\n```shell\ndocker pull hadrieng/insilicoseq:latest\n```\n\nFor more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)\n\n## Usage\n\nInSilicoSeq has two subcommands: `iss generate` to generate Illumina reads and `iss model` to create an error model from which the reads will take their characteristics.\n\nInSilicoSeq comes with pre-computed error models that should be sufficient for most use cases.\n\n### Generate reads with a pre-computed error model\n\nfor generating 1 million reads modelling a MiSeq instrument:\n\n```shell\ncurl -O -J -L https://osf.io/thser/download  # download the example data\niss generate --genomes SRS121011.fasta --model miseq --output miseq_reads\n```\n\nwhere `genomes.fasta` should be replaced by a (multi-)fasta file containing the reference genome(s) from which the simulated reads will be generated.\n\nInSilicoSeq comes with 3 error models: `MiSeq`, `HiSeq` and `NovaSeq`.\n\nIf you have built your own model, pass the `.npz` file to the `--model` argument to simulate reads from your own error model.\n\nFor 10 million reads and a custom error model:\n\n```shell\ncurl -O -J -L https://osf.io/thser/download  # download the example data\niss generate -g SRS121011.fasta -n 10m --model my_model.npz --output /path/to/my_reads\n```\n\ngranted you have built `my_model.npz` with `iss model` (see [below](#create-your-own-error-model))\n\nFor more examples and a full list of options, please refer to the full\n[documentation](http://insilicoseq.readthedocs.io)\n\n### Generate reads without input genomes\n\nWe can download some for you! InSilicoSeq can download random genomes from the ncbi using the infamous [eutils](https://www.ncbi.nlm.nih.gov/books/NBK25501/)\n\nThe command\n\n```shell\niss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads\n```\n\nwill generate 1 million reads from 10 random bacterial genomes.\n\nFor more examples and a full list of options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)\n\n### Create your own error model\n\nIf you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.\n\nSay you have a reference metagenome called `genomes.fasta`, and read pairs `reads_R1.fastq.gz` and `reads_R2.fastq.gz`\n\nAlign you reads against the reference:\n\n```shell\nbowtie2-build genomes.fasta genomes\nbowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \\\nsamtools view -bS | samtools sort -o genomes.bam\nsamtools index genomes.bam\n```\n\nthen build the model:\n\n```shell\niss model -b genomes.bam -o genomes\n```\n\nwhich will create a `genome.npz` file containing your newly built model\n\n## License\n\nCode is under the [MIT](LICENSE) license.\n\n## Issues\n\nFound a bug or have a question? Please open an [issue](https://github.com/HadrienG/InSilicoSeq/issues)\n\n## Contributing\n\nWe welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guidelines\n\n## Citation\n\nIf you use our software, please cite us!\n\n> Gourl\u00e9 H, Karlsson-Lindsj\u00f6 O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. _Bioinformatics_ (2018) doi:10.1093/bioinformatics/bty630\n\n\n",
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