pacbio-sequencing

There are 1 repository under pacbio-sequencing topic.

bcgsc / RNA-Bloom
:hibiscus: reference-free transcriptome assembly for short and long reads
denovo-assembly rna-seq single-cell-rna-seq bioinformatics-tool nanopore-sequencing bulk-rna-seq pacbio-sequencing
Language:Java 82
PacificBiosciences / MethBat
A battery of methylation tools for PacBio HiFi reads
hifi methylation pacbio-sequencing segmentation
16
WGLab / NanoRepeat
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
bioinformatics genome-analysis nanopore-sequencing repeat-detection short-tandem-repeats genomics pacbio-sequencing sequencing
Language:Python 15
zhixingfeng / iGDA
Detect and phase minor SNVs from long-read sequencing data
snvs oxford-nanopore pacbio-sequencing variants strains metagenome-deconvolution
Language:C++ 12
Mangul-Lab-USC / review-technology-dictates-algorithms
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.org/abs/2003.00110.
read-alignments needleman-wunsch smith-waterman heuristics read-mapping sequence-alignment hts nanopore-sequencing illumina-sequencing pacbio-sequencing hifi-read genome-analysis
Language:Jupyter Notebook 6
GDelevoye / SMSN
Re-implementation of J. Beaulaurier et al's SMSN strategy, using the default PacBio tools
bioinformatics pipeline analysis methylation methylation-analysis pacbio-sequencing
Language:Python 3
gauravcodepro / pangraphs-genome-assembly
genome assembly to pangraphs from illumina to long reads.
bioinformatics container-image containerization docker longread pacbio-data pacbio-iso-seq pacbio-sequencing
Language:Shell 2
RevantOrg / Revant
De novo repeat inference from long reads
repeats microsatellites transposons de-novo-assembly pacbio-sequencing bioinformatics
Language:Java 2
caspargross / expander
Identify and characterize repeat expansions in long read data
bioinformatics-pipeline nanopore-sequencing pacbio-sequencing repeats
Language:R 1
gauravcodepro / pacbio-nanopore-repeat-coverage
pacbio or oxford nanopore long reads repeat coverage estimation.
bioinformatics bioinformatics-algorithms bioinformatics-tool longread oxford-nanopore pacbio pacbio-sequencing sequencing-coverage sequencing-data sequencing-error
Language:Python 1
LRSDAY-Patch
nicolo-tellini / LRSDAY-Patch
Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.
bugfix genome-annotation genome-assembly nanopore-sequencing pacbio-sequencing yeast lrsday
Language:Shell 1
ibenjame / SM-PATseq
Snakemake workflow for SM-PATseq
pacbio pacbio-sequencing poly-a polyadenylation rna-seq
Language:R 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
bcftools for dealing with bcf files.
bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants
Language:Python
gauravcodepro / genomehifi-contiguity
a conda yaml for the genomehifi-contiguity analysis.
bioinformatics genome-analysis genome-assembly hifi pacbio pacbio-sequencing
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-string-extractions
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
long_read_polyATGC_trimmer using regular expression.
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