InSilicoSeq——微生物数据测序模拟工具

iss -h
usage: iss [subcommand] [options]

InSilicoSeq: A sequencing simulator

options:
  -h, --help     show this help message and exit
  -v, --version  print software version and exit

available subcommands:
  
    model        generate an error model from a bam file
    generate     simulate reads from an error model

usage: iss generate [-h] [--quiet | --debug] [--seed <int>] [--cpus <int>] [--genomes <genomes.fasta> [<genomes.fasta> ...]] [--draft <draft.fasta> [<draft.fasta> ...]] [--n_genomes <int>] [--ncbi [<str> ...]] [--n_genomes_ncbi [<int> ...]]
                    [--abundance <str> | --abundance_file <abundance.txt> | --coverage <str> | --coverage_file <coverage.txt> | --readcount_file <readcount.txt>] [--n_reads <int>] [--mode <str>] [--model <npz>] [--gc_bias] [--compress] --output <fastq>
                    [--sequence_type {metagenomics,amplicon}] [--fragment-length <int>] [--fragment-length-sd <int>] [--store_mutations]

simulate reads from an error model

arguments:
  --help,  -h           show this help message and exit
  --quiet, -q           Disable info logging. (default: False).
  --debug, -d           Enable debug logging. (default: False).
  --seed <int>          Seed all the random number generators
  --cpus <int>, -p <int>
                        number of cpus to use. (default: 2).
  --genomes <genomes.fasta> [<genomes.fasta> ...], -g <genomes.fasta> [<genomes.fasta> ...]
                        Input genome(s) from where the reads will originate
  --draft <draft.fasta> [<draft.fasta> ...]
                        Input draft genome(s) from where the reads will originate
  --n_genomes <int>, -u <int>
                        How many genomes will be used for the simulation. is set with --genomes/-g or/and --draft to take random genomes from the input multifasta
  --ncbi [<str> ...], -k [<str> ...]
                        Download input genomes from NCBI. Requires --n_genomes/-u option. Can be bacteria, viruses, archaea or a combination of the three (space-separated)
  --n_genomes_ncbi [<int> ...], -U [<int> ...]
                        How many genomes will be downloaded from NCBI. Required if --ncbi/-k is set. If more than one kingdom is set with --ncbi, multiple values are necessary (space-separated).
  --abundance <str>, -a <str>
                        abundance distribution (default: lognormal). Can be uniform, halfnormal, exponential, lognormal or zero-inflated-lognormal.
  --abundance_file <abundance.txt>, -b <abundance.txt>
                        abundance file for coverage calculations (default: None).
  --coverage <str>, -C <str>
                        coverage distribution. Can be uniform, halfnormal, exponential, lognormal or zero-inflated-lognormal.
  --coverage_file <coverage.txt>, -D <coverage.txt>
                        file containing coverage information (default: None).
  --readcount_file <readcount.txt>, -R <readcount.txt>
                        file containing read_count information (default: None).
  --n_reads <int>, -n <int>
                        Number of reads to generate (default: 1000000). Allows suffixes k, K, m, M, g and G (ex 0.5M for 500000).
  --mode <str>, -e <str>
                        Error model. If not specified, using kernel density estimation (default: kde). Can be kde, basic or perfect
  --model <npz>, -m <npz>
                        Error model file. (default: None). Use HiSeq, NextSeq, NovaSeq, MiSeq or Miseq-[20,24,28,32] for a pre-computed error model provided with the software, or a file generated with iss model. If you do not wish to use a model, use --mode basic or --mode
                        perfect. The name of the built-in models are case insensitive.
  --gc_bias, -c         If set, may fail to sequence reads with abnormal GC content. (default: False)
  --compress, -z        Compress the output in gzip format (default: False).
  --output <fastq>, -o <fastq>
                        Output file path and prefix (Required)
  --sequence_type {metagenomics,amplicon}, -t {metagenomics,amplicon}
                        Type of sequencing. Can be metagenomics or amplicon (default: metagenomics).
  --fragment-length <int>, -l <int>
                        Fragment length for metagenomics sequencing (default: None).
  --fragment-length-sd <int>, -s <int>
                        Fragment length standard deviation for metagenomics sequencing (default: None).
  --store_mutations, -M
                        Generates an additional VCF file with the mutations introduced in the reads

iss generate --seed 1234  --cpus 16 --genomes  SRS121011.fasta --model novaseq --n_reads 0.5M --output sample  --compress --sequence_type metagenomics --fragment-length 400  --fragment-length-sd 10

iss generate --seed 1234  --cpus 16 --genomes  SRS121011.fasta --abundance_file default_abundance.txt --model novaseq --n_reads 0.5M --output default  --compress --sequence_type metagenomics --fragment-length 400  --fragment-length-sd 10