{"repo":"nf-core/methylong","free":true,"listed":false,"github":"https://github.com/nf-core/methylong","clone":"git clone https://github.com/nf-core/methylong.git","description":"Extract methylation calls from long reads (ONT/ PacBio)","language":"Nextflow","stars":24,"topics":["nextflow","nf-core","pipeline","workflow","dna-methylation","fiber-seq","long-read","ont","pacbio"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/methylong is a bioinformatics pipeline that is tailored for long-read methylation calling. This pipeline requires a genome reference as input, and can take either modification-basecalled ONT reads, PacBio HiFi reads (modBam), raw sequencing Pod5 reads or raw Bam reads. The ONT workflow includes modcalling (optional), preprocessing (trim and repair) of reads, genome alignment and methylation calling. The PacBio HiFi workflow includes modcalling (optional), genome alignment and methylation calling. Methylation calls are extracted into BED/BEDGRAPH format, readily for direct downstream analysis. The downstream workflow includes SNV calling, phasing and DMR analysis. ONT workflow: 1. modcalling (optional) - basecall pod5 reads to modBam - dorado basecaller sup --modified-bases 5mC 5hmC (default) 2. trim and repair tags of input modBam - trim and repair workflow: 1. sort modBam - samtools sort 2. convert modBam to fastq - samtools fastq 3. trim barcode and adapters - porechop 4. convert trimmed modfastq to modBam - samtools import 5. repair MM/ML tags of trimmed modBam - modkit repair 3. align to reference (plus sorting and indexing) - dorado aligner ( default) / minimap2 - optional: remove previous alignment information before running dorado aligner using samtools reset - include alignment summary - samtools flagstat 4. create bedMethyl - modkit pileup , 5x base coverage minimum. 5. create bedgraphs (optional) PacBio workflow: 1. modcalling (optional) - modca","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/methylong/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}