Single-base-resolution detection of RNA epitranscriptomic modifications — from method to pipeline.

m5C-UBSseq stars since 2023
Ultrafast bisulfite sequencing for m5C detection

pseudoU-BIDseq stars since 2022
Detecting Ψ (pseudouridine) modification at single-base resolution

m6A-SACseq stars since 2022
Optimized protocol & pipeline for m6A-SAC-seq

m6A-CAMseq stars
Pipeline for m6A-CAM-seq

m6A-eTAMseq stars
Enzymatic method for assaying m6A at single-base resolution

pseudoU-PUMseq stars
Ψ-PUMseq pipeline for pseudouridine detection

dichromat stars new
Containerized conversion sequencing (eTAM-seq, CAM-seq, GLORI, BS-seq): mapping → site-calling → reporting

General pipelines for bioinformatics analysis (not RNA-modification detection).

SLOTH stars since 2018
Single-cell lineage tracing on Targeted Hypermutation

smallRNA-prism 🔒 WIP (not public yet)
Small RNA sequencing analysis pipeline — 🔒 WIP

scmd-calmorph stars since 2016
Quantify morphological traits of budding yeast

Bioinformatics tooling: alignment, QC, visualization & reporting.

countmut stars active
Unified ultra-fast strand-aware mutation counter — C core + Python wrapper; fuses pileup & read-walk counting, mate-overlap dedup, samtools-style -e/-p filters, base-count & allele/VCF output

coralsnake stars
Exon-aware RNA analysis pipeline — splice-aware BAM liftover, site/variant annotation, metagene & motif analysis (successor to metagene & variant)

sanger stars since 2018
Sanger sequencing toolkit — chromatogram visualization, mutation calling, QC, base-calling, trimming, assembly & export (CLI + Python + MCP)

cutseq stars
Trim sequencing adapters from NGS data automatically

igvplot stars new
IGV-style BAM read pileup / coverage / gene-feature / sashimi plots in matplotlib (pysam + dna_features_viewer), with per-base mismatch & epigenetic-modification detail

webblast
NCBI BLAST client CLI — submit, poll & cache web BLAST searches with colored output

Utilities & experiments

llmtop new
Real-time terminal dashboard for LLM inference servers (GPU, throughput, speculative decoding)

hey stars since 2018
Some useful / useless commands

graph-easy-py new
Python port of Graph::Easy — render graphs as ASCII art