🌺 reference-free transcriptome assembly for short and long reads

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.…

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

awk utilites for anlyzing pacbiohifi genomes and reads

a streamlit application for graphical analyisis of pacbiohifi reads

De novo repeat inference from long reads

go driven pacbiohifi sam sort for browser requests and caching

pacbio/oxford nanopore long reads repeat coverage estimation

streaming visualization of pacbiohifi reads

Identify and characterize repeat expansions in long read data

pacbiohifi report classifier for any sequencing startups

pacbioHifi genome assembly benchmarks

trimmomatic for long reads

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

Snakemake workflow for SM-PATseq

An accurate small variant representation unification method for multiple sequencing platforms

pacbiohifi view using awk

Detect and phase minor SNVs from long-read sequencing data

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

bash based fasta conversion of pacbiohifi reads and filtering.