Long read based human genomic structural variation detection with cuteSV

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

Pipeline to provide high accuracy single molecule consensus sequences from PacBio data using unique molecular identifiers (UMIs).

a complete workflow that can be dockerized for the long read assembly, it allows for the genome assembly update as well as it allows for the assembly from the start. if you have the illumina reads it allows for the genome mapping also

A workflow for processing CCS reads of AMF to ASVs using DADA2

The `pacmill` python package is a bioinformatics pipeline that is developed to process microbial 16S amplicon sequencing data and produce PDF reports detailing taxonomical assignments along with other statistics.

Hormiphora californensis genome annotation and supplemental materials related to the genome assembly.

A set of tootkit for dealing with COI amplicons using Pacbio sequencing platform

De novo repeat inference from long reads

SMP: A Salmonella Methylation analysis Pipeline

a streamlit component for reading and plotting the PacBioHiFi sequencing reads.

a slurm configuration analytical pipline for the analysis of the pacbiohifi sequencing genomes using the verkko, hifiasm and the genomeasm4pg. only provide the link to the sequencing or the files with the folder and rest it will do the work

a shell code getter for genomics alignments for the illumina and long reads from pacbio and the oxfordnanopore

a pacbiohifi read check for the quick view of the read types and making it easy for the fasta manipulations and read extractions. You can spawn also this in rust.

a pacbiohifi analyzer for pacbiohifi reads from sequence analysis to the graph alignments