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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...2305 days ago
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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...2339 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...2355 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...2314 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"2338 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...2107 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....780 days ago
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