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22 days ago
Juke34
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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
Full documentation here
Feedbacks and contributions are Welcome !