{"repo":"nf-core/pacvar","free":true,"listed":false,"github":"https://github.com/nf-core/pacvar","clone":"git clone https://github.com/nf-core/pacvar.git","description":"Longread PacBio sequencing processing for WGS and PureTarget","language":"Nextflow","stars":16,"topics":["alignment","long-read","pacbio","variant-calling","wgs","puretarget","nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/pacvar is a bioinformatics pipeline that processes long-read PacBio data. Specifically, the pipeline provides two workflows: one for processing whole-genome sequencing data, and another for processing reads from the PureTarget expansion panel offered by PacBio. This second workflow characterizes tandem repeats. Because the pipeline is designed for PacBio reads, it uses PacBio’s officially released tools. Preprocessing Overview 1. Demultiplex reads ( lima ) 2. Align reads ( pbmm2 ) 3. Sort and index alignments ( SAMtools ) WGS Workflow Overview 1. Choice of SNVs and small indels calling routes: a. DeepVariant (default) b. HaplotypeCaller 2. Choice of SV calling routes: a. sawfish (default) b. pbsv 3. Index pbsv 's VCF files ( bcftools ) 4. Phase SNVs, SVs and BAM files ( hiphase ) 5. CNV calling ( HiFiCNV ) 6. Extracts per-CpG methylation scores ( pb-CpG-tools::aligned bam to cpg scores ) 7. SNV, small indel, SV, and CNV annotation with Ensembl VEP [!TIP] Because sawfish consolidates both SV and CNV-related events, users may optionally disable the HiFiCNV step using --skip hificnv true when sawfish is selected as the SV caller to avoid redundant CNV analyses. [!NOTE] The Ensembl VEP integration in this pipeline does not bundle plugins or custom files. Also, the current VEP cache (115) does not support the CHM13 homo sapiens genome. If using CHM13 for the wgs workflow, disable VEP using --skip ensemblvep true . When using the default S3 VEP cache, avoid add","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/pacvar/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."}