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#+TITLE:  Sequence Read Simulator
#+AUTHOR: Petr Novak

Create pseudo short reads from long reads (Illumina Like). 

* Requirements
- python version > 3.4
- biopython

* Available tools
** long_reads_sampling
#+BEGIN_EXAMPLE

usage: long_reads_sampling.py [-h] [-i INPUT] [-o OUTPUT] [-l TOTAL_LENGTH]
                              [-s SEED]

Create sample of long reads, instead of setting number of reads to be sampled,
total length of all sampled sequences is defined

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        file with long reads in fasta format (default: None)
  -o OUTPUT, --output OUTPUT
                        Output file name (default: None)
  -l TOTAL_LENGTH, --total_length TOTAL_LENGTH
                        total length of sampled output (default: None)
  -s SEED, --seed SEED  random number generator seed (default: 123)
#+END_EXAMPLE

** long2short
#+BEGIN_EXAMPLE
usage: long2short.py [-h] [-i INPUT] [-o OUTPUT] [-cov COVERAGE]
                     [-L INSERT_LENGTH] [-l READ_LENGTH]

Creates pseudo short reads from long oxford nanopore reads

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        file with long reads in fasta format (default: None)
  -o OUTPUT, --output OUTPUT
                        Output file name (default: None)
  -cov COVERAGE, --coverage COVERAGE
                        samplig coverage (default: 0.1)
  -L INSERT_LENGTH, --insert_length INSERT_LENGTH
                        length of insert, must be longer than read length
                        (default: 600)
  -l READ_LENGTH, --read_length READ_LENGTH
                        read length (default: 100)

#+END_EXAMPLE
resulting reads in fasta format has names which include following information:
 - original long read name index
 - position of pseudo forward read in long reads
forward a reverse reads are interlaced a reverse reads are reverse complement of original long sequence
example outut:
#+BEGIN_EXAMPLE
>1_1_101_f
TGGTACTTGCGGTTACGTATTGCTAGCTAGTCTCCATTTGTCCGTTGGTCTTAGGTGATT
TTCCAAGCTTTGTGTGTAAATGTAAGGATCCTCATTTGTA
>1_1_101_r
GTTTTGTTATCGTGATCCACAGATCAGAAGATATCGCCGCTCACCTGTCAATTAATCTTA
ACTTAATGTACACTAGGGTTTTGGTTTTAACTGCTATCTT
>1_2001_2101_f
CTGAGTTGGGCAACATAGCCGACAAATTTGAACAATAAGCCGGTCCAGCCTTCTTTCTCA
GCTGATACATGAAACAAATCAAAGGAGCATTGTAAAGGCG
>1_2001_2101_r
TTTTGAATGATGGCACTACCGTGATCAAGGACGATGGTCTCCGTTCACTCGCTTTTGTTG
TACGTTCTCTATGAACTTGGTTTCTTTGCATTCGGTTCTT
>1_4001_4101_f
GAAGTTGAAGGAACATTTGGAAAGGTGTGTGAAGACTAATTTGGTCT
#+END_EXAMPLE