Not all are directly relevant, this has become somewhat of a reading list for myself.

• Sequence Alignment/Map Format Specification
• The Sequence Alignment/Map format and SAMtools
• Trimmomatic- a flexible trimmer for Illumina sequence data
• The khmer software package- enabling efficient nucleotide sequence analysis
• Disk-based k-mer counting on a PC
• Teaser- Individualized benchmarking and optimization of read mapping results for NGS data
• KMC 2- Fast and resource-frugal k-mer counting
• Snakemake—a scalable bioinformatics workflow engine
• Nextflowposterver3
• Rust-Bio- a fast and safe bioinformatics library
• Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards
• NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts.
• Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster
• A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
• near-optimal probabilistic rna-seq quantification - snakemake pipeline in repo - see this
• BioDB extractor: customized data extraction system for commonly used bioinformatics databases
• Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
• The Lair: A resource for exploratory analysis of published RNA-Seq data
• The gene cortex controls mimicry and crypsis in butterflies and moths