2932 days ago
3606 days ago
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...2327 days ago
2746 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...2361 days ago
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...2378 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...2337 days ago
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"2361 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...2129 days ago
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
2361 days ago
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2358 days ago
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....803 days ago
2182 days ago