Science Score: 36.0%
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Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
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○Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary
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Repository
:rocket: A sequencing simulator
Basic Info
- Host: GitHub
- Owner: HadrienG
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://insilicoseq.readthedocs.io
- Size: 9.47 MB
Statistics
- Stars: 207
- Watchers: 11
- Forks: 37
- Open Issues: 31
- Releases: 39
Topics
Metadata Files
README.md
InSilicoSeq
A sequencing simulator
InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.
InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided.
Installation
Insilicoseq is Available in bioconda.
To install with conda:
shell
conda install -c bioconda insilicoseq
Or with pip:
shell
pip install InSilicoSeq
Note: Insilicoseq requires python >= 3.5
Alternatively, with docker:
shell
docker pull quay.io/biocontainers/insilicoseq:2.0.0--pyh7cba7a3_0
For more installation options, please refer to the full documentation
Usage
InSilicoSeq 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.
InSilicoSeq comes with pre-computed error models that should be sufficient for most use cases.
Generate reads with a pre-computed error model
for generating 1 million reads modelling a MiSeq instrument:
shell
curl -O -J -L https://osf.io/thser/download # download the example data
iss generate --genomes SRS121011.fasta --model miseq --output miseq_reads
where genomes.fasta should be replaced by a (multi-)fasta file containing the reference genome(s) from which the simulated reads will be generated.
InSilicoSeq comes with 3 error models: MiSeq, HiSeq and NovaSeq.
If you have built your own model, pass the .npz file to the --model argument to simulate reads from your own error model.
For 10 million reads and a custom error model:
shell
curl -O -J -L https://osf.io/thser/download # download the example data
iss generate -g SRS121011.fasta -n 10m --model my_model.npz --output /path/to/my_reads
granted you have built my_model.npz with iss model (see below)
For more examples and a full list of options, please refer to the full documentation
Generate reads without input genomes
We can download some for you! InSilicoSeq can download random genomes from the ncbi using the infamous eutils
The command
shell
iss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads
will generate 1 million reads from 10 random bacterial genomes.
For more examples and a full list of options, please refer to the full documentation
Create your own error model
If you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.
Say you have a reference metagenome called genomes.fasta, and read pairs reads_R1.fastq.gz and reads_R2.fastq.gz
Align you reads against the reference:
shell
bowtie2-build genomes.fasta genomes
bowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \
samtools view -bS | samtools sort -o genomes.bam
samtools index genomes.bam
then build the model:
shell
iss model -b genomes.bam -o genomes
which will create a genome.npz file containing your newly built model
License
Code is under the MIT license.
Issues
Found a bug or have a question? Please open an issue
Contributing
We welcome contributions from the community! See our Contributing guidelines
Citation
If you use our software, please cite us!
Gourlé H, Karlsson-Lindsjö O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. Bioinformatics (2018) doi:10.1093/bioinformatics/bty630
Owner
- Name: Hadrien Gourlé
- Login: HadrienG
- Kind: user
- Location: Sweden
- Company: Folkhalsomyndigheten
- Website: www.hadriengourle.com
- Repositories: 53
- Profile: https://github.com/HadrienG
Bioinformatician, focusing on machine learning and building software for public health.
GitHub Events
Total
- Issues event: 5
- Watch event: 17
- Delete event: 2
- Issue comment event: 5
- Pull request event: 5
- Fork event: 5
- Create event: 2
Last Year
- Issues event: 5
- Watch event: 17
- Delete event: 2
- Issue comment event: 5
- Pull request event: 5
- Fork event: 5
- Create event: 2
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Hadrien Gourlé | g****n@g****m | 394 |
| dependabot-preview[bot] | 2****] | 31 |
| Hadrien Gourlé | h****e@u****e | 11 |
| dependabot[bot] | s****t@d****m | 8 |
| Étienne Mollier | e****r@m****g | 4 |
| Richel Bilderbeek | r****k | 1 |
| Daniel Standage | d****e@n****v | 1 |
| alienzj | a****j@g****m | 1 |
| Hadrien Gourlé | H****G | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 80
- Total pull requests: 64
- Average time to close issues: 9 months
- Average time to close pull requests: about 1 month
- Total issue authors: 68
- Total pull request authors: 12
- Average comments per issue: 2.13
- Average comments per pull request: 1.14
- Merged pull requests: 38
- Bot issues: 0
- Bot pull requests: 33
Past Year
- Issues: 8
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 9 months
- Issue authors: 8
- Pull request authors: 2
- Average comments per issue: 1.13
- Average comments per pull request: 0.5
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- HadrienG (4)
- gregoruar (3)
- izaak-coleman (2)
- dpellow (2)
- Tj-Idowu (2)
- slvrshot (2)
- Naturalist1986 (2)
- lmanchon (2)
- sergioSEa (2)
- vr1087 (1)
- cimendes (1)
- bramvandijk88 (1)
- dturaev (1)
- Shruteek (1)
- till-bornemann (1)
Pull Request Authors
- dependabot-preview[bot] (26)
- HadrienG (17)
- dependabot[bot] (13)
- ThijsMaas (12)
- StefanLelieveld (4)
- sebschmi (2)
- emollier (1)
- richelbilderbeek (1)
- pabviana (1)
- apcamargo (1)
- tessad (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 262 last-month
- Total dependent packages: 0
- Total dependent repositories: 4
- Total versions: 39
- Total maintainers: 1
pypi.org: insilicoseq
a sequencing simulator
- Homepage: https://github.com/HadrienG/InSilicoSeq
- Documentation: https://insilicoseq.readthedocs.io/
- License: MIT
-
Latest release: 2.0.1
published almost 2 years ago
Rankings
Maintainers (1)
Dependencies
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