Introduction

splitspliceleaderpe is a bioinformatics best-practice analysis pipeline for Split paired-end read files in two according to presence of splice leader in the first read..

The pipeline is built using Nextflow and used nf-core templates.

The SL.Oikopleura_diocia.arch file gives a example of architecture file for the splice leader of Oikopleura dioica:

tagdust -1 S:ACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG -2 R:N
tagdust -1 R:N

Pipeline summary

TBD

Pipeline test

The pipeline can be tested with a command like:

nextflow run ./main.nf --input input.test.csv -profile yourProfile -w path/to/your/scratch/area --arch SL.Oikopleura_diocia.arch --rrna OKIrRNA.fa

The main output files are in results/tagdust/. Reads with no splice leader are saved in *_SL_un_READ* and reads with splice leader in *_SL_READ*.