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Welcome to the HAMRLNC wiki!
For pipeline code visit the HARMLNC GitHub page.
- HAMRLNC is a multipurpose toolbox that expedites the analysis pipeline for HAMR, developed by Paul Ryvkin et al. HAMRLNC aims to make the original method more accessible by automating the tedious pre-processing steps and expanding on its functionalities with built-in post-processing steps, allowing users to visualize epitranscriptomic analysis with experimental condition contexts.
- HAMRLNC is high-throughput and performs RNA-modification annotation and long non-coding RNAs(lncRNA) annotation at a bioproject scale. HAMRLNC performs constitutive trimming of acquired reads using Trim-Galore, and makes use of STAR as the default aligning tool; mapped reads are pre-processed using selected methods from GATK, gffread, CPC2, infernal, samtools, etc. Users can also opt to quantify transcripts alongside these steps.
- HAMRLNC is optimized for partial parallel processing and modularization. Specifying a larger thread count where hardware permits will greatly increase the speed of a single run. If only partial functionality is needed (e.g. only analyzing modified ribonucleotides), users can implement flags to activate the function modules desired. See below for more details.
HAMRLNC workflow: Overview of the data flow of HAMRLINC. Possible entry points of pipeline in green with user icon. Intermediate file types and main pipeline in yellow. Major checkpoints in red, where users can resume without repeating previous steps. Clock icon indicates rate-determining steps.