Tag: FAST5

Data production Complete Y chromosomes from six different human haplogroups were isolated as previously described17 (Fig. 1a, b). In brief, chromosomes were obtained from lymphoblastoid cell lines (LCLs) used in the 1000 Genomes Project31 (1kgp) and sequenced on the ONT MinION. We also made use of the Y chromosome sorted ONT…

Hi all, I am expressing a GFP synonymous variant library in human cells and sequencing its RNA on the nanopore and I am having some trouble analysing the data. Initially, I basecalled all the fast5 files using the super accuracy model in the guppy basecaller, then I discarded the reads…

Convert Nanopore Fast5 files to Fasta format 0 Hi, Could anybody please suggest me a tool to convert the Nano-pore fast5 files to fasta files ? I have already tried Poretools and Nanopolish but wasn’t successful. I understand that fast5 can be converted to fastq directly but I need them…

Hello, I am having trouble running the GPU version of guppy on a cluster using SLURM. I have two guppy scripts called guppy_pass1.sh and guppy_pass2.sh. In the pass 1 script I basecall to get look at the ‘raw’ data without additional filtering/trimming. In the pass 2 script I basecall to…

FastQC Function AMPERE quality control tool for elevated throughput sequence data. Your Java What A match Java Runtime Ecology This Picard BAM/SAM Libraries (included in download) Code Maturation Robust. Mature code, but feedback exists comprehended. Code Released No, under GPL v3 or later. Initial Contact Simon Andrews Download Now Views…

Introduction Perturbations in the infant gut microbiome during early life affect growth, development, and long-term health (Sherman, 2010; Carl et al., 2014; Tarr and Warner, 2016). Preterm infants have a physiologically and anatomically immature gastrointestinal tract that is known to be more permeable than that of term infants, and their…

Best tool for trimming and filtering nanopore direct RNA sequencing. 1 Hello, I am new to analyzing long read data. I am trying to create a pipeline for analyzing data from Oxford Nanopore’s MinION Mk1b using the R.9.4.1 flow cell and using the Direct RNA Sequencing Kit. We used only…

I ran a nanopore sequencing on mk1c device with live basecalling and obtained some fastq in fastq_pass, fastq_fail folders. I tried to rerun the basecalling in a different machine, but found that they produce different sequences in just a test case, e.g.: In the fastq basecalled in mk1c > @b2e79451-050f-4d74-b091-40e6b6ee2229…

Cell lines and tissue culture The murine 17-CL1 cell line (derived from 3T3 cells, BEI Resources, Cat. No. NR-53719) was maintained in Dulbecco Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The NCTC clone 1469 cell line…

How to rerun Guppy Basecalling (with both fast5_pass and fast5_fail) 0 Hi, I recently started a nanopore sequencing and used the live-basecalling feature in mk1c. It was proceeding very slowly. I want to free up the machine to do more sequencing and am thinking of recovering the raw data in…

Enrichment in ONT amplicon sequencing and adaptive sequencing The number of TB reads detected in clinical samples can vary from one to thousands, with over 90% human reads8,9. To simulate a simple TB metagenomic sample for enrichment evaluation using MinION amplicon sequencing and adaptive sequencing, we prepared a synthetic metagenomic…

How to remove duplicate reads after ONT basecalling from fastq.gz files 1 Hi I ran into an error when my PC was halfway through basecalling, it errored on a fast5 file – number 577. I restarted basecalling from 578, and then when finished I basecalled 577 on its own. It…

A similar question has been already posted on the ONT community forum but without answers form guppy devs. I am using guppy 6.0.1 In short, when demultiplexing during basecalling using the options –do_read_splitting –detect_mid_strand_adapter –detect_mid_strand_barcodes ./guppy_basecaller -c dna_r9.4.1_450bps_sup.cfg -i $SCRATCH/barcode/fast5 -s $SCRATCH/barcode/fastq -x ‘auto’ –recursive –barcode_kits “EXP-NBD104” –trim_barcodes –trim_adapters –do_read_splitting…

Hi I’m new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi…

ONT analysis on Ubuntu 0 Hello guys, I am new on bioinformatic analysis of data from ONT (MinION with FLOW-MIN106D). The lab sent me a collection of fast5 files I have to analyze to obtain the metagenomic details (viruses). I have the new machine with on board Ubuntu 21 (Nvidia…

MinION Data Examples (FAST5) Database 0 Hello everyone, I am constructing a pipeline to analyze Oxford Nanopore MinION data. I have start from FAST5 files and for some optimizations I will try multiple tools for each step. So I will need several datasets to try. As I see most of…