28DDBJing_nagasaki.pdf

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3 de novo de novo

6 de novo (

http://p-galaxy.ddbj.nig.ac.jp de novo a b c Read set Overlap linear sequences by overlaps of k 1 to build graph components.

.. k 1 CAATG GCAAT CAATC T G C A C A Extend in k-mer space and break ties T G C A T A T C A T C G T C!

........... ATCGGAT... >a121:len = 5,845 >a122:len = 2,560 >a123:len = 4,443 >a124:len = 48 >a126:len = 66 Linear sequences.

.....attcgcaa...tcatcggat... Transcripts Figure 1 Overview of Trinity.

resulting in a collection of linear contigs (color lines, bottom), with each k-mer present only once in the contigs.

and then it builds individual de Bruijn graphs from each pool.

7 de novo a b c Read set Overlap linear sequences by overlaps of k 1 to build graph components... ATTCG TTCGC TCGCA CGCAA... CTTCG De Bruijn graph (k = 5)... k 1 CAATG GCAAT CAATC T G C A C A Extend in k-mer space and break ties T G C A T A T C A T C G T C! T G T* C k 1 k 1 k 1 k 1 AATGA ATGAT TGATC GATCG... A ATCGG TCGGA CGGAT AATCA ATCAT TCATC CATCG C TTCGCAA...T G... C Compacting Compact graph ATCGGAT... >a121:len = 5,845 >a122:len = 2,560 >a123:len = 4,443 >a124:len = 48 >a126:len = 66 Linear sequences... A G... C TTCGCAA...T C ATCGGAT... Finding paths Compact graph with reads Extracting sequences...cttcgcaa...tgatcggat......attcgcaa...tcatcggat... Transcripts Figure 1 Overview of Trinity. (a) Inchworm assembles the read data set (short black lines, top) by greedily searching for paths in a k-mer graph (middle), resulting in a collection of linear contigs (color lines, bottom), with each k-mer present only once in the contigs. (b) Chrysalis pools contigs (colored lines) if they share at least one k 1-mer and if reads span the junction between contigs, and then it builds individual de Bruijn graphs from each pool. (c) Butterfly takes each de Bruijn graph from Chrysalis (top), and trims spurious edges and compacts linear paths (middle). It then reconciles the graph with reads (dashed colored arrows, bottom) and pairs (not shown), and outputs one linear sequence for each splice form and/or paralogous transcript represented in the graph (bottom, colored sequences).

8 Tet raodon nigroviridis 2013 Aug;20(4):

10 DRA: RNAseq DRAweb DRASearchweb Organism:Tetraodon nigroviridis Search SRA Pipeline

11 DDBJ Import public DRA Input DRA/ERA/SRA Accession Number SRA Add my DRA entry Confirmation Send a mail when completed importing import OK importimport public DRA web DRAqueueddone

12 Trinity QV Preprocessing Private DRA entry SRAA FTP Tetraodon_nigroviridis_RNA-Seq Experimental ACCESION20122 NEXT

13 Trinity QV NEXT Trinity QV Run Preprocessing denovo Assemblly / mapping ID View

Trinity QV Count of QS Count 0.0e+00 2.0e+07 4.0e+07 6.

14 Trinity QV Count of QS Count 0.0e e e e e e e Phred Quality Score

Preprocessing Preprocessing Start Preprocessing

15 FASTQ/FASTADDBJ FTP FTP upload web HTTP upload DRA Private DRA entry Preprocessing Preprocessing Preprocessing Preprocessing Start Preprocessing PreprocesingID e.fastq.bz2 ID NEXT denovo Assembly Trinity NEXT

16 confirm NEXT Trinity.pl --seqtype fq --JM 100G --bflyheapspacemax 4G --bflygcthreads 1 --CPU 4 --single <> --output <> --min_contig_length 201

>m.565 g.565 ORF g.565 m.565 type:internal len:207 (-).

EYRRLLEGEAAASSSTSSTSSTKTRRL >m.566 g.566 ORF g.566 m.566 type:complete len:216 (+).

LAPPEVTMDPALAVQYEKELHVASQTALPDDEDDL* >m.568 g.568 ORF g.568 m.568 type:internal len:227 (-).

GDFTERLWAYLTIQQLLDKSKTGDAEEKANASAEALDMSLRYSFVTP >m.571 g.571 ORF g.571 m.571 type:5prime_partial len:394.

20 >m.565 g.565 ORF g.565 m.565 type:internal len:207 (-)... DLEMQIEGLKEELIFLKKNHEEELLAMRAQMSGQVHVEVEAAPAEDLTKVMADIREHYES ITAKNQKELETWFNSKSEALNKEMMTQTVTLQTSRSEVTEVKRSLQALQIELESLLGMKA SLEGTLQDTQNRYSMMLAGYQQQVTSLEQQLVQLRADLVRQGQDYQMLLDIKTRLELEIA EYRRLLEGEAAASSSTSSTSSTKTRRL >m.566 g.566 ORF g.566 m.566 type:complete len:216 (+)... MAQSVPVVMFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLFFNTNRGNVKF NVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCG NKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVEMPA LAPPEVTMDPALAVQYEKELHVASQTALPDDEDDL* >m.568 g.568 ORF g.568 m.568 type:internal len:227 (-)... GDRFKEDRKAKRLPEKSIDMIILLTDGDPNSGESRIPVIQENVKAAIGGQMSLFSLGFGN DVKYPFLDVMSRENNGLARRIYEGSDAALQLQGFYDEVSSPLLLDVDLRYPDNAVDSLTT NQFSQLFNGSEIVVAGRLKDNDIDNFPVEVFGQGLNDFSEQGQFSVLDWSGMYPDDDYIF GDFTERLWAYLTIQQLLDKSKTGDAEEKANASAEALDMSLRYSFVTP >m.571 g.571 ORF g.571 m.571 type:5prime_partial len: ASGGEGTHSSCGSWFNAGAKDFPSVPYSYLDFNDYKCKTSSGEIESYHDVHQVRDCRLVS LLDLALEKDYVRGKVADYMNRLVDMGVAGFRVDACKHMWPGDLSAVYGRLNNLNTKWFPE GSRPFIFQEVIDLGGEAISYTVYVHLGRVTEFKYGAKLGTVFRKWNNEKLMYTKNWGEGW GFMPNGNAVVFIDNHDNQRGHGAGGAAIVTFWDSRLHKMAVAYMLAHPYGVTRVMSSFRW NRHIVNGKDQNDWMGPPSHPDGSTKSVPINPDETCGDGWVCEHRWRQIKNMVIFRNVVNG QPHSNWWDNNSNQVAFGRGNRGFIIFNNDDWDLDVTLNTGLPAGTYCDVISGQKEAGRCT GKQIHVGSDGRAHFRISNRDEDPFVAIHVESKL* >m.573 g.573 ORF g.573 m.573 type:5prime_partial len: WEPSWPWQVSLQEYTGFHFCGGSLINENWVVTAAHCNVRTSHRVILGEHDRSSNNENIQV MQVGQVFKHPNYNSYTINNDITLIKLASPAQLNIRVSPVCVAETSDVFPGGMKCVTSGWG LTRYNAPDTPPRLQQVALPLLTNEECRKHWGSKITDLMVCAGASGASSCMGDSGGPLVCE KAGAWTLVGIVSWGSGFCSVSSPGVYARVTMLRAWMDQIIAAN* # --- full sequence best 1 domain domain number estimation ---- # target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target # Actin PF m.1-2.8e e Actin Apolipoprotein PF m.3-1.1e e Apolipoprotein A1/A4/E domain

22 DDBJ( New account UserID Registration e 1.FTP Upload 4

23 1.FTP clientpc DDBJFTP 2. FTP client Cyberduck

24 1.Cyberduck FTP-SSL(Explicit AUTH TLS) 4.( ) (21) 5.Pipeline guest 6. Query file Upload 1.Query submission DRA sample Bacillus subtilis subsp. natto BEST195 without plasmid pbest195l Read : 9,977,388 Read length : 36 2.Upload & 3.UploadPipeline

25 Query file Upload 1 1.Pipeline UploadSingle-end 2.Select a FASTA/FASTQ file UploadPaired-end 2.Select a FASTA/FASTQ file 3.Single-end 3.Paired-end 4.read 4.read1 file 5. 5.read1 fileread2 file Study title 3. 4.Assembly/Mapping

26 Query file Upload Upload 1.Upload FASTA/FASTQ(FTP client) 2. 3.

長崎は遺伝研大量遺伝情報研究室の所属です国立遺伝学研究所生命情報研究センター 3F 2F 欧州EBIと米国NCBIと密接に協力しながら DDBJ/EMBL/GenBank国際塩基配列データベースを構築しています私たちは塩基配列登録を支援するシステムづくり登録データの活用するシステムづく

長崎は遺伝研大量遺伝情報研究室の所属です国立遺伝学研究所生命情報研究センター 3F 2F 欧州EBIと米国NCBIと密接に協力しながら DDBJ/EMBL/GenBank国際塩基配列データベースを構築しています私たちは塩基配列登録を支援するシステムづくり登録データの活用するシステムづく AJACS十勝 (2014.09.12) DDBJ Read Annotation Pipeline の紹介と実習 (RNA-Seq配列のde novoアセンブリを中心に) 国立遺伝学研究所大量遺伝情報研究室長崎英樹長崎は遺伝研大量遺伝情報研究室の所属です国立遺伝学研究所生命情報研究センター 3F 2F 欧州EBIと米国NCBIと密接に協力しながら DDBJ/EMBL/GenBank国際塩基配列データ