1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.
2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs and HLA genes, which are not fully addressed in BWA-MEM2).
3. Sambamba markdup: Quickly marks or removes duplicate reads using Picard's criteria.
4. ichorCNA: Estimates the tumor DNA fraction in cell-free DNA from ultra-low-pass whole genome sequencing (0.1x coverage) based on copy number alterations (CNA).
5. Fragle: A deep learning method for quantifying ctDNA levels from cell-free DNA fragmentomic profiles. It detects TF as low as ~1% ctDNA and works with targeted genomic panel sequencing data.
6. AlfredQC: A quality control tool for high-throughput sequencing data. It assesses metrics like read quality scores, GC content, and duplication rates, visualized through detailed plots and summary statistics.
7. Mosdepth: A fast tool for calculating sequencing coverage depth, offering a quicker alternative to samtools/sambamba depth by processing BAM and CRAM files.
8. Bedtools: A versatile toolkit for genomics, enabling operations like intersect, merge, count, and shuffle on genomic intervals across formats such as BAM, BED, GFF/GTF, and VCF.
9. Datamash: A command-line tool for basic numeric, textual, and statistical operations on input data streams. It supports operations such as grouping, sorting, transposing, and performing arithmetic calculations on tabular data.
10. gwf.app: A pragmatic alternative to Snakemake. Developed at Aarhus University, this flexible, generic workflow tool builds and runs large scientific workflows.
