🌺 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

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

Identify and characterize repeat expansions in long read data

a streamlit application for graphical analyisis of pacbiohifi reads

pacbioHifi genome assembly benchmarks

trimmomatic for long reads

Snakemake workflow for SM-PATseq

streaming visualization of pacbiohifi reads

pacbio/oxford nanopore long reads repeat coverage estimation

codegetter for illumina, pacbio and oxford long read and short reads

polyATGC pacbio/oxford nanopore estimator

bash based fasta conversion of pacbiohifi reads and filtering.

pacbiohifi report classifier for any sequencing startups