🌺 reference-free transcriptome assembly for short and long reads

A battery of methylation tools for PacBio HiFi reads

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

Detect and phase minor SNVs from long-read sequencing data

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.…

An accurate small variant representation unification method for multiple sequencing platforms

Re-implementation of J. Beaulaurier et al's SMSN strategy, using the default PacBio tools

De novo repeat inference from long reads

reads to genome, pangenome graphs, summarize and analyze

MODIFI is for detecting DNA base modifications and linking ECEs to their microbial hosts using PacBio metagenomic data. It performs modification calling, motif discovery, and host–ECE association analysis, supporting both HiFi and subread data.

Identify and characterize repeat expansions in long read data

A pipeline for long-read sequencing data.

Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.

pacbioHifi genome assembly benchmarks

An awesome pipeline for processing bulk PacBio transcriptomics data generated with ISO-seq and MAS-seq.

Snakemake pipeline for Base and functional QC for Fiberseq analysis using PacBio and Nanopore data. This pipeline was designed for the Lab of Sebastian Pott at UC

Pipeline for Pre-processing for PacBio generated Fiber-seq Data, helps with 5mC and 6mA base modification calling, alignment, phasing and nucleosome calling. This pipeline was designed for the Lab of Sebastian Pott at UC

Studying the effect of long-read coverage on somatic structural variant calling from tissues

Snakemake workflow for SM-PATseq

rust enabled fastascan