AliNe is a pipeline written in Nextflow that focuses on the alignment process. It aligns reads to a reference genome using the tools of your choice among 16 different alignment tools (more to come).

AliNe supports short reads (both paired-end and single-end) as well as long reads generated by PacBio and Oxford Nanopore Technologies (ONT). It is designed to minimize user inputs and avoid common parameter mistakes ( e.g. scoring system, strandedness, orientation).

To try it you need Nextflow + Docker or Singularity.
Usage:

nextflow run Juke34/AliNe -r v1.1.0 -profile docker \
  --reads https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R1.fastq.gz \
  --genome https://raw.githubusercontent.com/Juke34/AliNe/refs/heads/main/test/yeast.fa \
  --read_type short_single \
  --aligner bbmap,bowtie,bowtie2,bwaaln,bwamem,bwasw,graphmap2,hisat2,kallisto,minimap2,ngmlr,nucmer,star,subread,sublong \
  --trimming_fastp \
  --fastqc \
  --samtools_stats

It has been published in JOSS: publication here.
Full documentation here.

Feedbacks and contributions are Welcome !