--- tags: GeneLab title: Generating in silico illumina reads --- > NOTE > Silvio's page generating the nanopore reads is here: https://hackmd.io/@SilvioWeging/generating-nanopore-reads # Generating in silico illumina reads [toc] ## Download results Made as shown below, can be downloaded with: ```bash curl -L -o simulated-bug-and-human-illumina-R1.fq.gz https://figshare.com/ndownloader/files/31454533 curl -L -o simulated-bug-and-human-illumina-R2.fq.gz https://figshare.com/ndownloader/files/31454530 ``` ## Making ### Starting data Created as documented here: https://hackmd.io/@astrobiomike/making-mock-human-and-microbe-fasta Downloading: ```bash curl -L -o mock-bug-and-human.fa.gz https://figshare.com/ndownloader/files/31454380 # gunzipping because the program used below doesn't take gzipped gunzip -f mock-bug-and-human.fa.gz ``` ### Env Conda install of [`inSilicoSeq`](https://github.com/HadrienG/InSilicoSeq#insilicoseq): ```bash conda create -y -n insilicoseq -c conda-forge -c bioconda -c defaults insilicoseq=1.4.6 biopython=1.77 conda activate insilicoseq ``` Fuller documentation of inSilicoSeq available [here](https://insilicoseq.readthedocs.io/en/latest/). ### Read generation Using packaged HiSeq error model. ```bash iss generate --seed 100 -p 4 --n_reads 100000 --draft mock-bug-and-human.fa --abundance uniform --model HiSeq --output simulated-bug-and-human-illumina -z # removing unzipped versions and renaming rm *.fastq mv simulated-bug-and-human-illumina_R1.fastq.gz simulated-bug-and-human-illumina-R1.fq.gz mv simulated-bug-and-human-illumina_R2.fastq.gz simulated-bug-and-human-illumina-R2.fq.gz ```