Closed pmenzel closed 3 years ago
Hi @pmenzel ,
That sounds interesting. We haven't tried with any of those kits or looked into the flongle unfortunately. I assume the data quality is similar?
Jody
Hi, I just wanted to piggy back on this thread. Does the tbprofiler support ONT reads after base calling? I am hoping to start some work on the Flongle and want to compare with my MiSeq runs.
Yep if you change the if you add --platform nanopore
it will switch to using nanopore optimised tools and parameters.
Let me know how you get along, I'd be interested to see how well nanopore performs vs Illumina.
oh amazing. I haven't started yet but planing to soon to compare ONT with previous Illumina. The plan is that for query DR isolates we get in the hospital I can run then quicker on a Flongle than batching on a MiSeq run! I'll keep you posted as and when I try!
Hey Jody,
Just confirm the command would be;
tb-profiler --nanopore profile -1 $sampleLoc/${sample}R1.fq.gz -2 $sampleLoc/${sample}R2.fq.gz -p $sample --dir $outputLoc
I have some Nanopore reads from last year that I was going to play around with!
Hi @peflanag,
Almost, usually we would just one set of reads so it should be somehting like:
tb-profiler profile --platform nanopore -1 $sampleLoc/${sample}.fq.gz -p $sample --dir $outputLoc
Jody
Sorry yes! I just did a copy and paste from one of my scripts and forgot that its one set of reads! I assume there's no need to run Unicycler to assemble and I can directly use the Fast5 files that where basecalled to Fastq?
Oh no it should just work direct with the fastq data!
Cool, I might give it a go today!
Dear Jody,
we are looking into sequencing MTB cultures with Nanopore, first with the MinION and possibly later with the Flongle.
I saw that in your 2019 paper, that you used the SQK-LWB001 kit from ONT. This low input DNA kit is no longer available, so I wanted to ask if you already tried some of the currently available kits? Probably many cultures would only yield low amounts of DNA, so that one likely needs a PCR-based kit, such as the Rapid PCR Barcoding Kit (SQK-RPB004) or the PCR Sequencing Kit (SQK-PSK004), which has higher yield in Gbp.
Second, the flongle seems quite useful for sequencing one or maybe two multiplexed samples at lower cost. Did you maybe already give it a try?
thanks and best wishes, Peter