Ukulandelelana kweMetagenomic-TGS
I-metagenome yingqokelela yezinto zemfuza zoluntu oluxubileyo lwezinto eziphilayo, ezifana neemetagenome zendalo kunye nezomntu. Iqulethe iigenome zeentsholongwane ezinokulinywa kunye nezingenakulinywa. Ukulandelelana kwe-metagenomic kwenza ukuba kufundwe ezi ndawo zintsonkothileyo ze-genomic ezifakwe kwiisampuli zendalo ngokubonelela ngeprofayili engaphezulu kwe-taxonomic. Ikwabonelela ngombono osebenzayo we-genomics ngokuhlola ii-genes ezifakwe kwi-encoded kunye neendima zazo ezibekayo kwiinkqubo zendalo. Ngelixa iindlela zendabuko ze-shotgun kunye ne-Illumina sequencing zisetyenziswe kakhulu kwizifundo ze-metagenomic, ukufika kwe-Nanopore kunye ne-PacBio sequencing efunde ixesha elide kuyitshintshile intsimi. Itekhnoloji ye-Nanopore kunye ne-PacBio iphucula uhlalutyo lwe-bioinformatic olusezantsi, ngakumbi ukuhlanganiswa kwe-metagenome, ukuqinisekisa ukuhlanganiswa okuqhubekayo. Iingxelo zibonisa ukuba i-metagenomics esekelwe kwi-Nanopore kunye ne-PacBio ziphumelele ukuvelisa ii-genome zebhaktheriya ezipheleleyo nezivaliweyo ezivela kwii-microbiomes ezintsonkothileyo (Moss, EL, et al., Nature Biotech, 2020). Ukudibanisa iiNanopore reads kunye neeIllumina reads kubonelela ngendlela enobuchule yokulungisa iimpazamo, ukunciphisa ukuchaneka okuphantsi kweNanopore. Olu dibaniselwano oluhambelanayo lusebenzisa amandla eqonga ngalinye lokulandelelana, lubonelela ngesisombululo esomeleleyo sokoyisa imida enokubakho kunye nokuphucula ukuchaneka kunye nokuthembeka kohlalutyo lwe-metagenomic.
Iqonga: I-Nanopore PromethION 48, i-Illumia kunye ne-PacBio Revio
Iimpawu zeNkonzo
● Ulandelelwano olude lokufunda kwiNanopore P48 (ilayibrari ye-10Kb); iPacBio Revio (ilayibrari ye-8Kb)
● Ukulungiswa kweempazamo: ukulandelelana kwi-Illumina NovaSeq (ilayibrari ye-PE150)
Iingenelo zeNkonzo
●Indibano yeMetagenome ekumgangatho ophezulu:Ngee-contigs ezimbalwa ezine-continuity ephezulu.
●Ukuchaneka Okuphezulu:Ukuchongwa kweentlobo kunye nokuqikelela i-gene esebenzayo.
●Ukuhlanganiswa Okuphuculweyo: Ukulungiselela ukwahlulwa kwe-genome yebhaktheriya kunye nohlalutyo lokuthelekisa i-metagenome.
●Uhlalutyo olupheleleyo lwe-Bioinformatics:Uhlalutyo lwethu alujolisanga kuphela kulwahlulo lwe-taxonomic kodwa lukwagxile kulwahlulo olusebenzayo loluntu.
●Amava amaninziIqela lethu lizisa amava amaninzi kwiprojekthi nganye, kunye nerekhodi yokuvala ngempumelelo iiprojekthi ezininzi ze-metagenomics kwiindawo ezahlukeneyo zophando kunye nokucubungula iisampulu ezingaphezu kwama-200,000, iqela lethu lizisa amava amaninzi kwiprojekthi nganye.
Iinkcukacha zeNkonzo
| Iqonga lokulandelelanisa | Icebo Lokulandelelanisa | Idatha iyacetyiswa |
| I-Illumina NovaSeq | PE150 | 6 Gb |
| I-Nanopore P48 | 10 kb | 6 / 10 Gb |
| Uhlaziyo lwePacBio | 8 kb | 10 / 20 Gb |
Iimfuno zeSampuli
| Uxinzelelo (ng/µL) | Isixa sisonke (µg) | Umthamo (µL) | |
| Ithala leeNcwadi le-Illumina PE150 | ≥1 | ≥0.03 | ≥20 |
| Ithala leencwadi leNanopore 10 kb | ≥40 | ≥2 | ≥20 |
| Ithala leencwadi le-PacBio le-8 kb | ≥50 | 10 µg/iseli | ≥20 |
Ukuhamba komsebenzi wenkonzo
Ukuhanjiswa kwesampulu
Ukwakhiwa kweThala leeNcwadi
Ukulandelelana
Uhlalutyo lwedatha
Iinkonzo zasemva kokuthengisa
Kubandakanya uhlalutyo olulandelayo:
● Ukulandelelanisa Ulawulo Lomgangatho Wedatha
● Ukuhlanganiswa kweMetagenome kunye nokuQaphela iGene
● Ingcaciso yeGene
● Uhlalutyo loBuqu beTaxonomic Alpha
● Uhlalutyo Lokusebenza Koluntu: Umsebenzi Webhayoloji, I-Metabolic, Ukumelana Nee-Antibiotic
● Uhlalutyo kwiMisebenzi yoBuntu kunye neyoBuntu boBuntu:
Uhlalutyo loBuntu beBeta
Uhlalutyo lwamaqela ahlukeneyo
Uhlalutyo lolwalamano: phakathi kwezinto ezingqongileyo kunye nokwakheka kunye nokwahluka kwe-OUT
Ukusasazwa kweseti yezakhi zofuzo ezingaphindi zisetyenziswe:
Isichazi-magama seGene: Indlela ye-KEGG
Isichazi-magama se-Gene: eggNOG
Isichazi-magama seGene: Iicarbohydrate ezi-CAZY
Uthungelwano lolwalamano lweentlobo:
Hlola uphuhliso oluququzelelwe yinkonzo yokulandelelana kwe-metagenomics ye-BMKGene kunye ne-Nanopore + Illumina ngale ncwadi iphambili:
UJin, H. et al. (2023) 'I-genome compendium esemgangathweni ophezulu ye-microbiome yamathumbu omntu yamaMongolia angaphakathi', i-Nature Microbiology 2023 8:1, 8(1), iphe. 150–161. doi: 10.1038/s41564-022-01270-1.
