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Обработка чтений

FastQC Trimmomatic Jellyfish. Обработка чтений. Velvet Ray SPAdes QUAST. Черновая сборка генома. CEGMA Scipio Augustus. Предсказание генов. Кластеризация ортологов. BLAST OrthoMCL. MAFFT trimAl SCaFoS RAxML Phylobayes MrBayes. Филогенетический анализ. FastQ. read :

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Обработка чтений

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  1. FastQC • Trimmomatic • Jellyfish Обработка чтений • Velvet • Ray • SPAdes • QUAST Черновая сборка генома • CEGMA • Scipio • Augustus Предсказание генов Кластеризация ортологов • BLAST • OrthoMCL • MAFFT • trimAl • SCaFoS • RAxML • Phylobayes • MrBayes • Филогенетический • анализ

  2. FastQ read : filtered : control# : index_sequence instrument : run# : flowcell_ID : lane : tile : x-pos : y-pos @HWI-ST992:147:D22HDACXX:8:2313:8106:8355 1:N:0:ATGTCA CCTCGTTAAGAATGAACGTAGGGAAGCCGTTAGGCATAGTTACGGAGACCCTTGCATAT + CCCFFFFFHHHHHJJJJJHIJJJJJJJJJHIIJJJJJJJIJJJJJGIGIJJJIJJJIJH @HWI-ST992:147:D22HDACXX:8:2313:8144:8417 1:N:0:ATGTCA ATAATGAATCTGAAATATAAATTTGGAATTATGATTTACAGATGTTCAAAACTTTGAAC + CCCFFFFFHHHGFIGGHIJIIIJJIEGHJGIHGIIGHIIJGJHGIGFIIGHJEHHIJIJ @HWI-ST992:147:D22HDACXX:8:2313:8391:8324 1:N:0:ATGTCA AGTCTATTTTTGAATTTAGTGGTATGACCAGGGCTACTACATTTTCCAATATCTTCCAA + CC@FFFFFHHHHFIJJJJJHIJFHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJ @HWI-ST992:147:D22HDACXX:8:2313:8483:8332 1:N:0:ATGTCA AAATTAATTACAGTTATTGTAATTATTATTATATATTAGGATGATTCACAAATTGGAAT + CCCFFFFFHGHHHIIIIJJGGHEIGIIJJJJJJJJIGIFIJIDGGJJIJJJJIGHJJII

  3. ASCII encoding 33 59 64 73 104 120 | | | | | | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwx SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS............................................... ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................ ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII................ .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ................ LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.............................................. 0........................26...31.......40 -5....0........9.............................40 0........9.............................40 3.....9.............................40 0........................26...31.........41 S - Sanger Phred+33, raw reads typically (0, 40) X - SolexaSolexa+64, raw reads typically (-5, 40) I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) http://en.wikipedia.org/wiki/FASTQ_format

  4. Phred quality score Q

  5. R1 R2

  6. Trimmomatic

  7. Mate-pair library Junction adapter (Nextera) Universal adapters

  8. Mate-pair library

  9. кратность к-мера

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