ARTIC Pipeline

Use when working with VILOCA, the viral haplotype reconstruction and mutation calling tool for short-read and long-read sequencing data. Covers the `viloca` CLI, `run` and `snv` subcommands, quality-s

3 shared topics • 2 shared operations

Pysam — Python interface to htslib for reading, writing, and manipulating SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, and tabix-indexed files. Provides Pythonic wrapper

2 shared topics • 3 shared operations

CNVkit -- Python toolkit for detecting copy number variants (CNVs) from targeted DNA sequencing data (hybrid capture, amplicon) and whole-genome sequencing (WGS). Leverages both on-target and off-targ

3 shared topics • 1 shared operation

nf-core/viralrecon — Nextflow pipeline for viral genome reconstruction and analysis from sequencing data. Supports Illumina and Oxford Nanopore reads for SARS-CoV-2, influenza, and other viral genomes

3 shared topics • 1 shared operation

VarScan2 -- Java-based variant caller for somatic and germline SNV/indel detection, copy number analysis, and LOH detection from samtools mpileup output. Supports tumor-normal paired somatic calling,

3 shared topics • 1 shared operation