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README.mason_frag_sequencing.md

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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
  +
  HHHIIHHHHIHHHIHGFHIGHIEGGHGIFIIFHHHIIHIGCFEEIGIIIHIIECGFIDIDIEDABFGIIEFHIHAI<IIIHAIEHIH>ICIHIGGIIIIG
  @simulated.3
  TGCTATTAGGTTCAGGCTCATTATCGGAAACAGGACCTAAAAACAACAAAATATTATTTTTCACTGCTTAAGAAAAAAAAATCACCTCCCACCTCCCATA