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pacbio-data

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tjiangHIT /cuteSV

Long read based human genomic structural variation detection with cuteSV

oxford-nanopore structural-variation pacbio-data

UpdatedMar 13, 2025
Python

bcgsc /arcs

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

science c-plus-plus bioinformatics genome graph assembler scaffold oxford-nanopore 10xgenomics pacbio-data nanopore-sequencing

UpdatedNov 6, 2024
C++

HiPhase

PacificBiosciences /HiPhase

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

variants phasing pacbio-data hifi structural-variants short-tandem-repeats

UpdatedSep 25, 2024
Rust

deepomicslab /SpecHLA

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.

nanopore cancer phase immunity hla-typing pacbio-data local-assembly loh haplotype reads-binning hla-sequence loss-of-heterozygosity genotype-frequency allelic-imbalance human-leukocyte-antigens

UpdatedFeb 18, 2025
C++

LRSDAY

yjx1217 /LRSDAY

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

genomics genome-annotation oxford-nanopore genome-assembly yeast pacbio-data yeastgenome

UpdatedMar 4, 2024
Perl

tjiangHIT /rMETL

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

mei variant-calling transposons pacbio-data nanopore-sequencing realignment mei-detection

UpdatedAug 13, 2024
Python

hitbc /rMETL

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

mei variant-calling pacbio-data nanopore-sequencing

UpdatedOct 4, 2019
Python

niaid /UMI-pacbio-pipeline

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

pacbio umi pacbio-data network-filtering unique-molecular-identifiers

UpdatedFeb 5, 2025
Python

xapple /pacmill

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.

bioinformatics-pipeline dna-sequences pacbio-data 16s-rrna pdf-reports

UpdatedMay 19, 2022
Python

IBCHgenomic /panscape

reads to genome, pangenome graphs, summarize and analyze

bioinformatics pacbio-data nanopore-sequencing nanopore-reads pacbio-sequencing

UpdatedFeb 26, 2025
Rust

KatjaKo /PacBio_AMF

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

dada2 pacbio-data amplicon-sequence-variants arbuscular-mycorrhizal-fungi

UpdatedOct 18, 2022
R

hormiphora

conchoecia /hormiphora

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

annotation genomics hi-c pacbio pacbio-data ctenophora

UpdatedOct 9, 2020
HTML

comery /HIFI-barcode-pacbio

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

perl barcode pacbio-data

UpdatedJan 24, 2019
Perl

fcunial /Revant

De novo repeat inference from long reads

repeats microsatellite transposon de-novo-assembly pacbio-data

UpdatedJul 21, 2021
Java

AukeHaver /salmonella_methylation_pipeline

SMP: A Salmonella Methylation analysis Pipeline

annotation epigenetics de-novo-assembly pacbio-data hybrid-assembly

UpdatedJan 28, 2021
R

IBCHgenomic /pacbiohifi-read-analyzer

pacbiohifi read analyzer using recursion

bioinformatics pacbio pacbio-data bioinformatics-tool pacbio-hifi-sequencing-reads pacbiohifi

UpdatedAug 17, 2024
Python

jacobwindsor /SQANTIExplorer

Inter-sample analysis of SQANTI classifications

bioinformatics rna-seq liftover tgs pacbio rna-sequencing genome-browser pacbio-data bioinformatics-tool bioinformatics-visualization pacbio-iso-seq sqanti

UpdatedAug 12, 2020
R

IBCHgenomic /genomeassembly-pacbiohifi

pacbioHifi genome assembly benchmarks

bioinformatics bioinformatics-data genome-sequencing genome-analysis genome-assembly pacbio-data genome-alignment pacbio-sequencing

UpdatedOct 4, 2024
HTML

IBCHgenomic /pacbiohifi-report-classifier

pacbiohifi report classifier for any sequencing startups

bioinformatics python3 genome-analysis pacbio-data pacbio-sequencing pacbiohifi

UpdatedAug 17, 2024
Python

IBCHgenomic /pacbio-polyATGC-remove

polyATGC pacbio/oxford nanopore estimator

bioinformatics genome-annotation genome-analysis pacbio-data pacbio-sequencing pacbio-hifi-sequencing-reads pacbiohifi

UpdatedAug 20, 2024
Python

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