pacbio-data

There are 1 repository under pacbio-data topic.

tjiangHIT / cuteSV
Long read based human genomic structural variation detection with cuteSV
structural-variation pacbio-data oxford-nanopore
Language:Python 232
bcgsc / arcs
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
c-plus-plus science bioinformatics assembler scaffold genome 10xgenomics graph nanopore-sequencing oxford-nanopore pacbio-data
Language:C++ 91
HiPhase
PacificBiosciences / HiPhase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
hifi pacbio-data phasing short-tandem-repeats structural-variants variants
Language:Rust 55
LRSDAY
yjx1217 / LRSDAY
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
genomics genome-assembly genome-annotation pacbio-data oxford-nanopore yeastgenome yeast
Language:Perl 30
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.
hla-typing haplotype loh hla-sequence nanopore pacbio-data phase cancer local-assembly reads-binning allelic-imbalance genotype-frequency loss-of-heterozygosity immunity human-leukocyte-antigens
Language:C++ 22
tjiangHIT / rMETL
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
variant-calling pacbio-data nanopore-sequencing mei realignment transposons mei-detection
Language:Python 15
hitbc / rMETL
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
variant-calling pacbio-data nanopore-sequencing mei
Language:Python 6
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
Language:Python 4
gauravcodepro / pangraphs-genome-assembly
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
bioinformatics container-image containerization docker longread pacbio-data pacbio-iso-seq pacbio-sequencing
Language:Shell 2
comery / HIFI-barcode-pacbio
A set of tootkit for dealing with COI amplicons using Pacbio sequencing platform
pacbio-data barcode perl
Language:Perl 1
hormiphora
conchoecia / hormiphora
Hormiphora californensis genome annotation and supplemental materials related to the genome assembly.
annotation ctenophora genomics hi-c pacbio pacbio-data
Language:HTML 1
KatjaKo / PacBio_AMF
A workflow for processing CCS reads of AMF to ASVs using DADA2
amplicon-sequence-variants arbuscular-mycorrhizal-fungi dada2 pacbio-data
Language:R 1
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.
16s-rrna bioinformatics-pipeline dna-sequences pacbio-data pdf-reports
Language:Python 1
AukeHaver / salmonella_methylation_pipeline
SMP: A Salmonella Methylation analysis Pipeline
epigenetics annotation de-novo-assembly hybrid-assembly pacbio-data
Language:R 0
fcunial / Revant
De novo repeat inference from long reads
de-novo-assembly microsatellite pacbio-data repeats transposon
Language:Java 0
gauravcodepro / pacbiohifi-analyzer
a pacbiohifi analyzer for pacbiohifi reads from sequence analysis to the graph alignments
bioinformatics genome-assembly pacbio-data pacbio-iso-seq pacbiohifi
Language:Ruby 0
gauravcodepro / alignments-code-generator
code getter for illumina, pacbio, oxford long reads alignments.
illumina illumina-sequencing oxford-nanopore pacbio-data pacbio-hifi-sequencing-reads pacbio-sequencing
Language:Shell
gauravcodepro / awk-pacbiohifi
awk code for pacbiohifi alignments from verkko and other genome assembly methods
awk-language awk-programming-language awk-script genome-analysis genome-assembly hifi pacbio-data pacbio-sequencing
Language:Awk
gauravcodepro / bcftools-filter
making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.
bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants
Language:Python
gauravcodepro / gawk-awk-paf-alignments
gawk and awk combined functions for working with pacbiohifi aligned data.
gawk genome-analysis genome-assembly genome-sequencing pacbio-data paf
Language:Awk
gauravcodepro / lastz-alignment-awk
lastz alignment sorting and plotting the alignment length
genome-analysis genomealignment hifi pacbio-data pacbio-sequencing
Language:Awk
gauravcodepro / pacbio-nanopore-polyATGC-trimmer
A regular expression based polyATGC trimmer for the long reads or the fastq reads extremely fast and returns a fasta and also a dataframe for the sequence classification
bioinformatics fasta-sequences longread oxford-nanopore pacbio-data trimming-bases
Language:Python
gauravcodepro / pacbio-nanopore-string-extractions
A implication of stringr package to calculate the pattern detection in R using the stringR package for the pacbio and the oxford nanopore reads
bioinformatics oxford-nanopore pacbio pacbio-data pacbio-sequencing pattern-matching pattern-recognition rprogramming
Language:R
gauravcodepro / pacbio-polyATGC-trimmer-recursion
a shorter version of the long_read_polyATGC_trimmer after implementing a array recompile and storing the variables while running a subtle part of the recursion.
bioinformatics fasta-sequences oxford-nanopore pacbio-data pacbio-sequencing pattern-matching trimming-bases
Language:Python
gauravcodepro / pacbiohifi-read-assimilator
a pacbiohifi read check for the quick view of the read types.
fasta-sequences fastq-files genome-analysis hifi pacbio-data pacbio-sequencing pangenome
Language:Shell
gauravcodepro / pacbiohifi-universitat-potsdam
pacbiohifi sequencing genomes analysis using the verkko, hifiasm and the genomeasm4pg.
genome-annotation genome-assembly genome-sequencing pacbio-data pacbio-sequencing slurm-cluster slurm-job slurm-workload-manager
Language:Shell
gauravcodepro / streamlit-pacbiohifi
a streamlit component for reading and plotting the PacBioHiFi sequencing reads.
pacbio-data pacbiohifi streamlit streamlit-application streamlit-webapp
Language:Python
jacobwindsor / SQANTIExplorer
Inter-sample analysis of SQANTI classifications
rna-seq rna-sequencing tgs pacbio pacbio-data pacbio-iso-seq bioinformatics bioinformatics-tool bioinformatics-visualization sqanti genome-browser liftover
Language:R

pacbio-data

tjiangHIT / cuteSV

bcgsc / arcs

PacificBiosciences / HiPhase

yjx1217 / LRSDAY

deepomicslab / SpecHLA

tjiangHIT / rMETL

hitbc / rMETL

niaid / UMI-pacbio-pipeline

gauravcodepro / pangraphs-genome-assembly

comery / HIFI-barcode-pacbio

conchoecia / hormiphora

KatjaKo / PacBio_AMF

xapple / pacmill

AukeHaver / salmonella_methylation_pipeline

fcunial / Revant

gauravcodepro / pacbiohifi-analyzer

gauravcodepro / alignments-code-generator

gauravcodepro / awk-pacbiohifi

gauravcodepro / bcftools-filter

gauravcodepro / gawk-awk-paf-alignments

gauravcodepro / lastz-alignment-awk

gauravcodepro / pacbio-nanopore-polyATGC-trimmer

gauravcodepro / pacbio-nanopore-string-extractions

gauravcodepro / pacbio-polyATGC-trimmer-recursion

gauravcodepro / pacbiohifi-read-assimilator

gauravcodepro / pacbiohifi-universitat-potsdam

gauravcodepro / streamlit-pacbiohifi

jacobwindsor / SQANTIExplorer