pacbio

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Here are 62 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 Apr 15, 2020
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 Sep 2, 2020
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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 Sep 3, 2019
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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 Sep 3, 2020
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PacificBiosciences / blasr

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BLASR: The PacBio® long read aligner

bioinformatics alignment long-read pacbio blasr

Updated Jun 4, 2020
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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 Aug 28, 2020
Jupyter Notebook

PacificBiosciences / GenomicConsensus

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PacBio® variant and consensus caller

bioinformatics arrow consensus pacbio variant-calling polish

Updated Apr 25, 2019
Python

ruanjue / smartdenovo

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Ultra-fast de novo assembler using long noisy reads

assembler pacbio

Updated Feb 19, 2018
C

chhylp123 / hifiasm

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Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

bioinformatics genomics pacbio denovo-assembly hifi-read

Updated Aug 28, 2020
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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 Jul 30, 2020

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 / IsoSeq

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

clustering discovery pacbio rna isoforms polishing

Updated Mar 18, 2020

marbl / Winnowmap

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Long read / genome alignment software

nanopore pacbio genome-analysis

Updated Aug 20, 2020
C

mortazavilab / TALON

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Technology agnostic long read analysis pipeline for transcriptomes

pacbio transcriptome oxford-nanopore transcript-quantification

Updated Aug 28, 2020
Python

adigenova / wengan

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An accurate and ultra-fast hybrid genome assembler

nanopore pacbio hybrid illumina genome-assembler

Updated May 25, 2020
Perl

PacificBiosciences / barcoding

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Lima - Demultiplex Barcoded PacBio Samples

single-molecule barcode pacbio lima demultiplexing

Updated Feb 18, 2020
R

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
C

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 Jan 27, 2020
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

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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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 dna-sequencing

Updated Aug 30, 2020

PacificBiosciences / minorseq

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Minor Variant Calling and Phasing Tools

statistics next-generation-sequencing haplotypes long-read pacbio minor-variant phasing drug-resistance

Updated Apr 22, 2020

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 27, 2020
Python

PacificBiosciences / smrtflow

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SMRT Link and Analysis Server, PacBio Scala analysis tools and Common models

commandline scala swagger pacbio pbsmrtpipe

Updated Oct 23, 2018
Scala

bpucker / MGSE

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Mapping-based Genome Size Estimation

genomics genome ngs plants pacbio illumina genome-assembly read-mapping ont nanopore-sequencing genome-size-estimation

Updated Oct 29, 2019
Python

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 Aug 28, 2020
Jupyter Notebook

bioinformatist / py3_scripts

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Life is short, *****.

crawler scrapy pacbio blast gtf

Updated Jan 9, 2017
Python

Magdoll / CoSA

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Coronavirus (SARS-Cov-2) sequencing analysis

pacbio long-reads long-read-sequencing covid19 sars-cov-2

Updated Jul 15, 2020
Python

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