Results for "ONT"
Users
About me: An academic pursuit that will leverage the managerial, analytical and entrepreneurial skills I have gained during my education and internships to contribute towards the growth of the organization and my own in the service of community.2916 days ago
- About me: .... and loving guy who also seeks divine love from others .... And I also like finding connections in the unexpected. Any questions or curiosities? contact me.
3590 days ago
- +4 more Users
Blogs
Bioinformatics tools developed for Oxford Nanopore data analysis !
...ce data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, whic...2311 days ago
Bookmarks
- ...as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, another...
2729 days ago
ONT assembly and Illumina polishing pipeline
...wing steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the...2345 days ago
- +14 more Bookmarks
Top-level pages
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...De novo genome assembly MHAP Produces highly continuous assembly (fully resolve...Miniasm Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Con...assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimens...2361 days ago
Run miniasm assembler on nanopore reads !
...the raw input reads. Find the detail of the reads repeats: fq2fa ONT_A.fastq ONT_A.fasta minimap2 -xava-o...AONTself30000final.eps minidot -f 5 -m 20000 AONTself.paf > AONTself20000.eps sed 's/_tem...2320 days ago
- +3 more Top-level pages
Wire posts
Bio-Scripts
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2344 days ago
Long reads mapper bash script !
...r.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scri...r.sh minimap2 ref.fa reads.fa/fq 48 ont" exit 1 fi fileName=...dex $refFasta if [ $readsType == "ont" ]; then $lamsaLoc aln...o "NGMLR:Please specify reads type: ont, pacbio" fi elif [ $toolNa...2113 days ago
- +1 more Bio-Scripts
Tags
ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...Tags: ONT, assembly, Illumina, polishing, pipeline
2345 days ago
- When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the options: spades.py This produces: SPAdes genome ...
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2341 days ago
- +17 more Tags
Comments
Comment on "Run miniasm assembler on nanopore reads !"
minimap2 –x ava-ont \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./minimap....786 days ago
- ...ta with prefix “meta”. We estimate the genome size, tell canu NOT to use HPC (as we don’t have one for porecamp) and give it some ONT data as fasta. This runs pre...
2165 days ago
- +2 more Comments
