BBDuk

EAGER2 / nf-core/eager — reproducible Nextflow pipeline for ancient DNA (aDNA) and palaeogenomics. Handles adapter trimming with AdapterRemoval2, read merging, low-complexity filtering, mapping with B

2 shared topics • 2 shared operations

Guppy — Oxford Nanopore Technologies neural-network basecaller for converting raw nanopore signal data (FAST5/POD5) into nucleotide sequences (FASTQ/BAM). Supports GPU-accelerated basecalling, barcodi

2 shared topics • 2 shared operations

Oxford Nanopore Technologies (ONT) sequencing data analysis skill. Covers the end-to-end nanopore pipeline: basecalling raw POD5/FAST5 signal with Dorado, long-read alignment with Minimap2, haploid co

3 shared topics

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format, demultiplexing sequencing runs by index sequences, or trimming adapters from short-read data. Handles HiSeq, MiSeq, NextSeq,

2 shared topics • 1 shared operation

Human Cell Atlas (HCA) tools — programmatic access to the HCA Data Portal, Data Coordination Platform (DCP), and matrix service for single-cell genomics datasets. Covers the hca Python CLI client, Azu

2 shared topics • 1 shared operation