https://github.com/seqan/mason
Tools for Biological Sequence Simulation
https://github.com/seqan/mason
Last synced: 4 months ago
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Tools for Biological Sequence Simulation
- Host: GitHub
- URL: https://github.com/seqan/mason
- Owner: seqan
- License: other
- Created: 2023-05-16T09:35:47.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2023-05-17T14:50:56.000Z (about 3 years ago)
- Last Synced: 2026-02-11T02:26:33.546Z (4 months ago)
- Language: HTML
- Size: 6.45 MB
- Stars: 8
- Watchers: 5
- Forks: 4
- Open Issues: 2
-
Metadata Files:
- Readme: README.mason_frag_sequencing.md
- License: LICENSE
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README
# Mason Fragment Sequencing
## Overview
The program `mason_frag_sequencing` is a simple sequence simulator. Instead of the
end-to-end read simulator `mason_simulator`, the program
`mason_frag_sequencing` expects as the input DNA fragment. For these
fragments, sequencing is then simulated either from one or both ends.
The program thus exposes the NGS sequencing engine of the Mason package
without fragment selection and variant simulation.
## Examples
### Help
The command:
```
$ mason_frag_sequencing --help
```
prints the help for Mason Genome.
### Simulating Paired-End Reads from Fragments
We call `mason_frag_sequencing` on the file adeno_fragments.fa to simulate
paired-end Illumina reads (default) of length 100.
```
$ head adeno_fragments.fa
>fragment0
CCTATCTAATAATATACCTTATACTGGACTAGTGCCAATATTAAAATGAAGTGGGCGTAGTGTGTAATTT
GATTGGGTGGAGGTGTGGCTTTGGCGTGCTTGTAAGTTTGGGCGGATGAGGAAGTGGGGCGCGGCGTGGG
AGCCGGGCGCGCCGGATGTGACGTTTTAGACGCCATTTTACACGGAAATGATGTTTTTTGGGCGTTGTTT
GTGCAAATTTTGTGTTTTAGGCGCGAAAACTGAAATGCGGAAGTGAAAATTGATGACGGCAATTTTATTA
TAGGC
>fragment1
ACGGGGAAACTCCACGTTGGCGCTCAAAGGGCGCGTTTATTGTTCTGTCAGCTGATCGTTTGGGTATTTA
ATGCCGCCGTGTTCGTCAAGAGGCCACTCTTGAGTGCCAGCGAGAAGAGTTTTCTCTGCCAGCTCATTTT
CACGGCGCCATTATGAGAACTGAAATGACTCCCTTGGTCCTGTCGTATCAGGAAGCTGACGACATATTGG
$ mason_frag_sequencing -i adeno_fragments.fa -o left.fq -or right.fq
...
$ head left.fq
@simulated.1
GCCTATAATAAAATTGCCGTCATCAATTTTCACTTCCGCATTTCAGTTTTCGCGCCTAAAACACAAAATTTGCACAAACAACGCCCAAAAAACATCATTT
+
IIIHHIHIHIIIIIHHHHIIHGIGGIIIHIGIIFGEIIICGIHHIFFIEIFIHCHFFEIIEHFHIIHIAIIDDIGIHIIIHIIHFIIDBFHDHIIIAIDI
@simulated.2
GGCAACTCTGGATGGTCTAACTGAAACTCCTCACGTTCCCTATCAGCGGCAGCAGCAGCTGCGGATGCAGAAACATGCGCCATTCCGTTCTCGTCTTGCT
+
IHIIHIHHIHIIIHHHHIIHFHHGFIIHGIIIGHIIEGIHIHHHEGGIIIGGIIIIDGBIIIIICIDDEICGIFII=IIEHFDDHIIIIIII;DAGEBI?
@simulated.3
AGTCCTGTGAGCACCACCGGAATAGTACTGGAAATACTGACTTAATGTGCTCTTTGTGCTATCTGCGAGCCTACAACATGTTCATTTACAGTAAGTGTGC
$ head right.fq
@simulated.1
CCTATCTAATAATATACCTTATACTGGACTAGTGCCAATATTAAAATGAAGTGGGCGTAGTGTGTAATTTGATTGGGTGGAGGTGTGGCTTTGGCGTGCT
+
HHHHHIIHIHIHHIHHHIHHIIIFIHHHHIIIIGIGHIIIIEHIIIHHIIIBHHIIIHFIG?IIFIHGIGGIGDEBGIE?IHDEIIII?IIIGIC@IAIB
@simulated.2
ACGGGGAAACTCCACGTTGGCGCTCAAAGGGCGCGTTTATTGTTCTGTCAGCTGATCGTTTGGGTATTTAATGCCGCCGTGTTCGTCAAGAGGCCACTCT
+
HHHIIHHHHIHHHIHGFHIGHIEGGHGIFIIFHHHIIHIGCFEEIGIIIHIIECGFIDIDIEDABFGIIEFHIHAIICIHIGGIIIIG
@simulated.3
TGCTATTAGGTTCAGGCTCATTATCGGAAACAGGACCTAAAAACAACAAAATATTATTTTTCACTGCTTAAGAAAAAAAAATCACCTCCCACCTCCCATA
```