Tool:AliNe (Alignment in Nextflow)

Question

[Juke34]

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 !

[Charles Plessy]

Maybe you would be interested in adding LAST to the collection of aligners? You can see in https://nf-co.re/pairgenomealign how I run in a whole-genome alignment pipeline.

[Juke34]

I standardize the output for all aligner in sorted bam file. It is why it is specific to “read” alignment. I don’t think we can output bam with last. It exists already the pairgenomealign nf-core pipeline for whole genome alignment.

[Charles Plessy]

Indeed, LAST outputs to MAF. However it also provides a maf-convert command that does SAM, whose output can be piped in samtools view for BAM or CRAM output. LAST has been used to align Nanopore RNA reads to genomes, for instance.

[Juke34]

Then yes it is feasible. Thx for the information

Answer 1

[Juke34]

Lastis now present in AliNe v1.3.0
Before that bwa-mem2 and salmon have been added in AliNe v1.2.0