bbmap

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.

Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease

Count the occurrences of reference sequences in sequencing reads (fastq) or genome assemblies (fasta), with Seal from BBTools

Nextflow (nf-core) workflow for mapping reads to large collections of genomes.

Proof of concept of a SRA to trimmed FASTQ (including quality control) pipeline with Nextflow

Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.