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1 #+TITLE: Sequence Read Simulator
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2 #+AUTHOR: Petr Novak
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3
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4 Create pseudo short reads from long reads (Illumina Like).
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5
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6 * Requirements
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7 - python version > 3.4
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8 - biopython
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9
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10 * Available tools
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11 ** long_reads_sampling
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12 #+BEGIN_EXAMPLE
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13
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14 usage: long_reads_sampling.py [-h] [-i INPUT] [-o OUTPUT] [-l TOTAL_LENGTH]
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15 [-s SEED]
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16
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17 Create sample of long reads, instead of setting number of reads to be sampled,
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18 total length of all sampled sequences is defined
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19
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20 optional arguments:
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21 -h, --help show this help message and exit
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22 -i INPUT, --input INPUT
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23 file with long reads in fasta format (default: None)
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24 -o OUTPUT, --output OUTPUT
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25 Output file name (default: None)
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26 -l TOTAL_LENGTH, --total_length TOTAL_LENGTH
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27 total length of sampled output (default: None)
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28 -s SEED, --seed SEED random number generator seed (default: 123)
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29 #+END_EXAMPLE
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30
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31 ** long2short
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32 #+BEGIN_EXAMPLE
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33 usage: long2short.py [-h] [-i INPUT] [-o OUTPUT] [-cov COVERAGE]
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34 [-L INSERT_LENGTH] [-l READ_LENGTH]
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35
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36 Creates pseudo short reads from long oxford nanopore reads
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37
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38 optional arguments:
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39 -h, --help show this help message and exit
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40 -i INPUT, --input INPUT
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41 file with long reads in fasta format (default: None)
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42 -o OUTPUT, --output OUTPUT
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43 Output file name (default: None)
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44 -cov COVERAGE, --coverage COVERAGE
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45 samplig coverage (default: 0.1)
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46 -L INSERT_LENGTH, --insert_length INSERT_LENGTH
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47 length of insert, must be longer than read length
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48 (default: 600)
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49 -l READ_LENGTH, --read_length READ_LENGTH
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50 read length (default: 100)
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51
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52 #+END_EXAMPLE
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53 resulting reads in fasta format has names which include following information:
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54 - original long read name index
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55 - position of pseudo forward read in long reads
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56 forward a reverse reads are interlaced a reverse reads are reverse complement of original long sequence
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57 example outut:
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58 #+BEGIN_EXAMPLE
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59 >1_1_101_f
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60 TGGTACTTGCGGTTACGTATTGCTAGCTAGTCTCCATTTGTCCGTTGGTCTTAGGTGATT
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61 TTCCAAGCTTTGTGTGTAAATGTAAGGATCCTCATTTGTA
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62 >1_1_101_r
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63 GTTTTGTTATCGTGATCCACAGATCAGAAGATATCGCCGCTCACCTGTCAATTAATCTTA
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64 ACTTAATGTACACTAGGGTTTTGGTTTTAACTGCTATCTT
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65 >1_2001_2101_f
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66 CTGAGTTGGGCAACATAGCCGACAAATTTGAACAATAAGCCGGTCCAGCCTTCTTTCTCA
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67 GCTGATACATGAAACAAATCAAAGGAGCATTGTAAAGGCG
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68 >1_2001_2101_r
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69 TTTTGAATGATGGCACTACCGTGATCAAGGACGATGGTCTCCGTTCACTCGCTTTTGTTG
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70 TACGTTCTCTATGAACTTGGTTTCTTTGCATTCGGTTCTT
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71 >1_4001_4101_f
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72 GAAGTTGAAGGAACATTTGGAAAGGTGTGTGAAGACTAATTTGGTCT
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73 #+END_EXAMPLE
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