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Mimick is a simulator for linked-read FASTQ data. It started its life as XENIA, a module in VISOR, and has since added features and perks. Mimick allows you to simulate an arbitrary number of haplotypes, set overall coverage, molecule coverage, and mix-match barcodes with linked-read chemistries.
It's simple, really. This software mimics linked-read data, Pavel has an affinity for naming software after fictional monsters and "mimick" (with a "k") is the old-English spelling of the word, leaving mimic available for some other bioinformatician to use for a less farcical reason. Despite the lore of mimics being deadly traps, this software is anything but, we promise.
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Supported Linked-Read Types:
- 10X
- Haplotagging
- stLFR
- TELLseq
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Get Started
See the installation and usage guides, then call up mimick in the command line to be greeted with:
Usage: mimick [OPTIONS] BARCODES FASTA...
Simulate linked-read FASTQ using genome haplotypes. Barcodes can be supplied one of two ways:
1 let Mimick randomly generate barcodes based on a specification of length,count
• two integers, comma-separated, no space
• e.g. 16,400000 would generate 400,000 unique 16bp barcodes
2 you can provide a file of specific nucleotide barcodes, 1 per line
You can specify the linked-read barcode chemistry to simulate via --lr-type as well as the output
format of FASTQ files (default is the same as barcode type). For example, you can generate 96 barcodes
(common haplotagging style), select --lr-type stlfr (combinatorial 3-barcode on R2 read), and have
--output-type tellseq (@seqid:barcode header format).
--lr-type Format
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
10x/tellseq single barcode on R1
haplotagging R1 and R2 each have different combinatorial 2-barcodes
stlfr combinatorial 3-barcode on R2
--output-type Barcode Location Example
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
10x start of R1 sequence ATAGACCATAGAGGACA...
haplotagging sequence header as BX:Z:ACBD @SEQID BX:Z:A0C331B34D87
standard sequence header as BX:Z:BARCODE, no specific format @SEQID BX:Z:ATACGAGACA
stlfr appended to sequence ID via #1_2_3 @SEQID#1_354_39
tellseq appended to sequence ID via :ATCG @SEQID:TATTAGCAC
╭─ General Options ────────────────────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
│ --circular -C contigs are circular/prokaryotic │
│ --output-prefix -o output file prefix │
│ [default: simulated/SIM] │
│ --output-type -O output format of FASTQ files │
│ --quiet -q 0 all output, 1 no progress bar, 2 no output │
│ [default: 0] │
│ --regions -r one or more regions to simulate, in BED format │
│ --seed -S random seed for simulation │
│ --threads -t number of threads to use for simulation │
│ [default: 2; x>=1] │
│ --version Show the version and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Read Simulation Parameters ─────────────────────────────────────────────────────────────────────────╮
│ --coverage mean coverage target for simulated data │
│ [default: 30.0; x>=0.05] │
│ --distance outer distance between the two ends in bp │
│ [default: 500; x>=0] │
│ --error base error rate │
│ [default: 0.02; 0<=x<=1] │
│ --extindels indels extension rate │
│ [default: 0.25; 0<=x<=1] │
│ --indels indels rate │
│ [default: 0.15; 0<=x<=1] │
│ --lengths length of R1,R2 reads in bp │
│ [default: 150,150] │
│ --mutation mutation rate │
│ [default: 0.001; x>=0] │
│ --stdev standard deviation of --distance │
│ [default: 50; x>=0] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Linked Read Parameters ─────────────────────────────────────────────────────────────────────────────╮
│ --combinatorial -b treat barcodes as combinatorial with this many segments │
│ [default: haplotagging] │
│ --molecule-attempts -a how many tries to create a molecule with <70% ambiguous bases │
│ [default: 300; x>=5] │
│ --molecule-coverage -c mean percent coverage per molecule if <1, else mean number of reads per │
│ molecule │
│ [default: 0.2; x>=1e-05] │
│ --molecule-length -m mean length of molecules in bp │
│ [default: 80000; x>=650] │
│ --molecules-per -n mean number of unrelated molecules per barcode per chromosome, where a │
│ negative number (e.g. -2) will use a fixed number of unrelated molecules │
│ and a positive one will draw from a Normal distribution │
│ [default: 2] │
│ --singletons -s proportion of barcodes will only have a single read pair │
│ [default: 0; 0<=x<=1] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────╯
Documentation: https://pdimens.github.io/mimick/
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