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- Utilising QIIME 2 pipeline: a current and future golden standard . . .
QIIME 2 is nowadays used as a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed As a powerful, scalable and decentralized microbiome analysis resource, it emphasizes transparency in data analysis of Amplicon-Seq data (e g 16S rRNA gene) , and pays more attention to interactive and
- Dada2 in Qiime2: losing reads during merging - Biostar: S
qiime deblur denoise-16S --i-demultiplexed-seqs demux-joined-filtered qza --p-trim-length 140 --p-sample-stats --p-jobs-to-start 4 --o-representative-sequences rep-seqs qza --o-table table qza --o-stats deblur-stats qza; As a result, I got even worse results than dada2 I would be glad for any advice on merging my readings
- Qiime Vs Mothur : Why Use One Over The Other? - Biostar: S
QIIME is a python interface (glue) that connects a very large number of disparate programs and what QIIME really does is transforms the input outputs of these and allows you to feed one program into the other You will need to install a very large number of dependent programs to use QIIME
- QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data . . .
I am struggling to pre-process my 16S rRNA gene amplicon Illumina Sequencing data using QIIME I have several issues that I can't find clear answers for on QIIME's website I have 4 files from the sequencing - read 1, read 2, index 1 and index 2 (MiSeq Paired End - 2x 250 cycle)
- Validate QIIME pipeline using 16S rDNA amplicon data (Illumina MiSeq . . .
Recently, I’ve been used QIIME to analyze 16S rRNA gene amplicons, from environmental seawater samples (9 in total), sequenced using Illumina MiSeq platform I used paired-end sequencing to target the V4-V6 (partially) hypervariable region of 16S rDNA using the universal primers 515YF-Y906R-jed
- QIIME2 Vs MetaPhlAn3
The biggest difference is qiime is used on amplicon sequencing data, while MetaPhlAn is for shotgun metagenomics data
- How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using . . .
I know this's an old question, but many people face this same mapping file issue fairly often This is a link to QIIME's support site explaining how to deal with Illumina paired-end output (only to extend nkuyfq answer): http: qiime org tutorials processing_illumina_data html
- losing large amount of reads when using Qiime2 vsearch joinpairs command
import with qiime tools import trim with command cutadapt trim-paired join with command vsearch join-pairs filter with command quality-filter q-score
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