pacbio

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Here are 79 public repositories matching this topic...

ruanjue / wtdbg2

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Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

nanopore assembly alignment pacbio

Updated Feb 6, 2021
C

fritzsedlazeck / Sniffles

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Structural variation caller using third generation sequencing

bioinformatics nanopore pacbio bioconda structural-variations structural-variation ngm-lr

Updated Dec 18, 2020
C++

philres / ngmlr

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NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

docker mapper next-generation-sequencing alignment long-read pacbio bioconda oxford-nanopore structural-variations

Updated Aug 16, 2021
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chanzuckerberg / shasta

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De novo assembly from Oxford Nanopore reads.

nanopore assembly sequencing dna long-read pacbio de-novo

Updated Dec 3, 2021
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chhylp123 / hifiasm

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Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

bioinformatics genomics pacbio denovo-assembly hifi-read

Updated Nov 29, 2021
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Nextomics / NextDenovo

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Fast and accurate de novo assembler for long reads

assembler pacbio oxford-nanopore genome-assembly long-reads

Updated Oct 13, 2021

Genetalks / gtz

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A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

gene compression nanopore sam pacbio compress bam fastq genomic-data-compression compression-rate fastq-compression gtx

Updated Oct 19, 2021

PacificBiosciences / blasr

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BLASR: The PacBio® long read aligner

bioinformatics alignment long-read pacbio blasr

Updated Aug 18, 2021
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marbl / Winnowmap

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Long read / genome alignment software

nanopore pacbio genome-analysis

Updated Nov 26, 2021
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sequana / sequana

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Sequana: a set of Snakemake NGS pipelines

coverage rna-seq snakemake taxonomy ngs pacbio variant-calling de-novo sequanix

Updated Dec 8, 2021
Jupyter Notebook

ruanjue / smartdenovo

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Ultra-fast de novo assembler using long noisy reads

assembler pacbio

Updated Feb 24, 2021
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PacificBiosciences / GenomicConsensus

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PacBio® variant and consensus caller

bioinformatics arrow consensus pacbio variant-calling polish

Updated Apr 25, 2019
Python

PacificBiosciences / IsoSeq

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IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

clustering discovery pacbio rna isoforms polishing

Updated Apr 1, 2021

adigenova / wengan

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An accurate and ultra-fast hybrid genome assembler

nanopore pacbio hybrid illumina genome-assembler

Updated Dec 15, 2020
Perl

PacificBiosciences / ccs

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CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

machine-learning bioinformatics consensus pacbio variant-calling ccs

Updated Sep 30, 2021

mortazavilab / TALON

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Technology agnostic long read analysis pipeline for transcriptomes

pacbio transcriptome oxford-nanopore transcript-quantification

Updated Sep 7, 2021
Python

vpc-ccg / haslr

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A fast tool for hybrid genome assembly of long and short reads

bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

Updated Apr 22, 2020
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lfaino / LoReAn

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Long Reads Annotation pipeline

rna-seq nanopore annotations pacbio

Updated Sep 1, 2020
Python

PacificBiosciences / barcoding

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Lima - Demultiplex Barcoded PacBio Samples

single-molecule barcode pacbio lima demultiplexing

Updated Nov 22, 2021
R

mortazavilab / TranscriptClean

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Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome

sam pacbio oxford-nanopore

Updated Nov 1, 2021
Python

vpc-ccg / lordfast

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Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

mapping long-read pacbio oxford-nanopore single-molecule-sequencing

Updated Jul 15, 2019
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parklab / xTea

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Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

nanopore pacbio illumina transposable-elements xtea linked-reads

Updated May 12, 2021
Python

andrewjpage / tiptoft

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Predict plasmids from uncorrected long read data

bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

Updated Dec 5, 2019
Python

ganlab / GALA

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Long-reads Gap-free Chromosome-scale Assembler

nanopore pacbio scaffolding genome-analysis genome-assembly long-reads gap-filling

Updated Aug 11, 2021
Python

Nazeeefa / awesome-sequencing-tech-papers

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A collection of publications on comparison of high-throughput sequencing technologies.

bioinformatics nanopore genomics sequencing pacbio awesome-list genome-sequencing illumina sequence-alignment illumina-sequencing dna-sequencing hifi human-genomes long-read-sequencing

Updated Nov 22, 2021

mortazavilab / swan_vis

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A Python library to visualize and analyze long-read transcriptomes

bioinformatics long-read pacbio transcriptome oxford-nanopore pacbio-iso-seq

Updated Dec 1, 2021
Jupyter Notebook

PacificBiosciences / pbsmrtpipe

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PacBio Workflow Engine

pipeline pacbio pbsmrtpipe

Updated Oct 24, 2018
Python

adigenova / fast-sg

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Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

nanopore pacbio scaffolding illumina genome-assembly hybrid-genome-assembly alignment-free-algorithm

Updated May 29, 2018
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a-ludi / dentist

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Close assembly gaps using long-reads at high accuracy.

docker bioinformatics snakemake cluster singularity dub pacbio dentist genome-assembly daligner long-reads gap-filling gaps low-complexity-regions snakemake-workflow close-assembly-gaps damapper snakemake-cluster

Updated Dec 9, 2021
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fmalmeida / MpGAP

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Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

nanopore pipeline nextflow reproducible-research reproducible-science pacbio polish illumina spades genome-assembly hybrid-assemblies unicycler flye canu pilon

Updated Nov 26, 2021
Nextflow

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