De novo Bacterial Genome Assembly
Peb muab kev pabcuam sib sau ua ke ntawm cov kab mob genome tiav, lav 0 qhov sib txawv. Qhov no ua tau los ntawm kev koom ua ke cov thev naus laus zis nyeem ntev, xws li Nanopore thiab PacBio rau kev sib dhos thiab kev nyeem luv luv nrog Illumina rau kev lees paub kev sib dhos thiab kev kho qhov yuam kev ntawm ONT nyeem. Peb qhov kev pabcuam muab cov txheej txheem bioinformatic tiav los ntawm kev sib dhos, kev sau ntawv ua haujlwm, thiab kev tshuaj xyuas bioinformatic siab heev, ua tiav cov hom phiaj tshawb fawb tshwj xeeb. Qhov kev pabcuam no ua rau muaj kev txhim kho cov genomes siv tau rau ntau yam kev tshawb fawb txog genetic thiab genomic. Tsis tas li ntawd, nws tsim lub hauv paus rau cov ntawv thov xws li kev ua kom zoo dua qub, kev tsim kho genetic, thiab kev tsim kho thev naus laus zis microbial, ua kom ntseeg tau tias cov ntaub ntawv genomic txhim khu kev qha thiab tsis muaj qhov sib txawv tseem ceeb rau kev txhim kho kev nkag siab txog kev tshawb fawb thiab kev tsim kho tshiab biotechnological.
Cov yam ntxwv ntawm kev pabcuam
● Muaj ob txoj kev xaiv uas koj xaiv tau nyob ntawm seb koj xav tau qib kev ua tiav ntawm cov genome.
● Kev Xaiv Qauv Genome: Kev nyeem luv luv sequencing nrog Illumina NovaSeq PE150.
● Ua tiav 0 qhov sib txawv genome.
● Kev nyeem ntev txog Nanopore PromethION 48 lossis PacBio Revio rau kev sib sau ua ke ntawm genome.
● Kev nyeem luv luv sequencing ntawm Illumina NovaSeq rau kev lees paub genome thiab kho qhov yuam kev (Nanopore) lossis los tsim ib daim ntawv qauv genome.
Cov Kev Pabcuam Zoo
●Kev lav phib xaub rau Genome Zero-GapQhov no yog vim muaj kev koom ua ke ntawm Illumina sequencing nrog long read sequencing (Nanopore lossis PacBio).
●Kev Ua Haujlwm Bioinformatics Tag Nrho:Qhov no suav nrog kev sib sau ua ke ntawm genome thiab kev kwv yees ntawm ntau yam genomic elements, kev piav qhia txog cov gene annotation, thiab genome visualisations xws li Circos plot.
●Kev Paub Ntau YamBMKGENE muaj ntau tshaj 20,000 hom kab mob me me uas tau sib sau ua ke, thiab muaj ntau tshaj kaum xyoo ntawm kev paub dhau los, pab pawg neeg tshuaj xyuas uas muaj kev txawj ntse heev, cov ntsiab lus dav dav, thiab kev txhawb nqa tom qab muag zoo heev.
●Kev Txhawb Nqa Tom Qab Muag Khoom:Peb txoj kev cog lus tseem ceeb tshaj qhov ua tiav qhov project nrog rau 3 lub hlis kev pabcuam tom qab muag. Thaum lub sijhawm no, peb muab kev saib xyuas project, kev pab daws teeb meem, thiab cov lus nug thiab lus teb los teb cov lus nug ntsig txog cov txiaj ntsig.
●Muaj ntau txoj kev npaj ua sequencing:Rau ntau lub hom phiaj tshawb fawb sib txawv thiab cov kev xav tau ntawm kev ua tiav ntawm genome.
Cov Lus Qhia Txog Kev Pabcuam
| Kev Pabcuam | Txoj Kev Npaj Txog Sequencing |
| Daim Ntawv Qhia Txog Genome | Illumina PE150 100x |
| 0 Qhov Sib Txawv Genome | Nanopore 100x + Illumina PE150 100x Or Pacbio HiFi 30x + Illumina PE150 100x (xaiv tau) |
Cov Qauv Yuav Tsum Tau Ua:
| Kev Ntsuas (ng/µL) | Tag nrho cov nqi (µg) | Ntim (µL) | OD260/280 | OD260/230 | |
| PacBio | ≥20 | ≥1.2 | ≥20 | 1.7-2.2 | ≥1.0 |
| Nanopore | ≥40 | ≥2 | ≥20 | 1.7-2.2 | 1.0-3.0 |
| Illumina | ≥1 | ≥0.06 | ≥20 | - | - |
· Cov kab mob: ≥3.5x1010 cov hlwb
Kev Ua Haujlwm Pabcuam
Kev xa khoom qauv
Kev tsim kho tsev qiv ntawv
Kev txheeb xyuas kab ke
Kev tshuaj xyuas cov ntaub ntawv
Cov kev pab cuam tom qab muag
Muaj xws li Kev Tshawb Fawb Hauv Qab No:
● Kev Tswj Xyuas Zoo ntawm Cov Ntaub Ntawv Sequencing
● Kev Sib Sau Ua Ke ntawm Genome
● Kev Tshawb Fawb Txog Cov Cheebtsam Genome: Kev Kwv Yees Txog CDS thiab ntau yam Cheebtsam Genomic
● Cov lus piav qhia ua haujlwm nrog ntau lub ntaub ntawv dav dav (GO, KEGG, thiab lwm yam) thiab cov ntaub ntawv siab heev (CARD, VFDB, thiab lwm yam)
● Kev Pom Kev Genome
Peb muab cov genome hauv hom ntawv fasta uas yooj yim nkag tau thiab cov ntaub ntawv genome annotation (gff).
Kev piav qhia txog noob caj noob ces - MUS
Kev piav qhia txog noob caj noob ces - CAZY carbohydrates
Kev pom Genome - Circos plot
Tshawb nrhiav cov kev nce qib uas tau pab txhawb los ntawm BMKGene cov kev pabcuam sib sau ua ke ntawm cov kab mob genome los ntawm kev sau cov ntawv tshaj tawm uas tau xaiv los ntawm ntau tus neeg.
Dai, W. et al. (2023) 'Kev Tshawb Pom Bacteroides uniformis F18-22 ua ib qho Probiotic Bacterium uas muaj kev nyab xeeb thiab tshiab rau kev kho mob ntawm Ulcerative Colitis los ntawm Tib Neeg Txoj Hnyuv Noj Qab Haus Huv',Phau Ntawv Xov Xwm Thoob Ntiaj Teb ntawm Kev Tshawb Fawb Txog Molecular, 24(19), nplooj 14669. doi: 10.3390/IJMS241914669/S1.
Kang, Q. et al. (2021) 'Cov kab mob Proteus mirabilis uas tiv taus ntau yam tshuaj uas nqa blaOXA-1 thiab blaNDM-1 los ntawm cov tsiaj qus hauv Suav teb: ua rau muaj kev pheej hmoo rau kev noj qab haus huv pej xeem ntau ntxiv',Kev Tshawb Fawb Txog Tsiaj Txhu Sib Koom Ua Ke, 16(6), pp. 798–809. doi: 10.1111/1749-4877.12510 ib.
Wang, TT et al. (2017) 'Cov kab ke genome tiav ntawm endophyte Bacillus flexus KLBMP 4941 qhia txog nws txoj kev loj hlob ntawm cov nroj tsuag thiab cov hauv paus caj ces rau kev kam rau ntsev',Phau ntawv Journal of Biotechnology, 260, pp. 38–41. doi: 10.1016/J.JBIOTEC.2017.09.001.
Wang, X. et al. (2021) 'Cov Plasmids Tiv Thaiv Ntau Tus Qauv ntawm Klebsiella Ua Rau Muaj Kev Sib Kis Ntau ntawm Cov noob Antimicrobial',Cov ciam teb hauv Microbiology, 12, ib. 754931. doi: 10.3389/FMICB.2021.754931/BIBTEX.
