{"repo":"nf-core/methylseq","free":true,"listed":false,"github":"https://github.com/nf-core/methylseq","clone":"git clone https://github.com/nf-core/methylseq.git","description":"Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair","language":"Nextflow","stars":197,"topics":["nf-core","nextflow","workflow","bisulfite-sequencing","dna-methylation","methyl-seq","pipeline","em-seq","epigenome","epigenomics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/methylseq is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity / Podman / Charliecloud / Apptainer containers making installation trivial and results highly reproducible. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the nf-core website. Read more about Bisulfite Sequencing & Three-Base Aligners used in this pipeline here Pipeline Summary The pipeline allows you to choose between running either Bismark, bwa-meth / MethylDackel or BWA-Mem plus rastair for TAPS data processing. rastair can also be used with bwa-meth aligned reads by setting the aligner to --aligner bwameth and adding the flag --taps . Choose between workflows by using --aligner bismark (default, uses bowtie2 for alignment), --aligner bismark hisat , --aligner bwameth or --aligner bwamem . For higher performance, t","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/methylseq/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."}