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ruanjue / wtdbg2

237

A fuzzy Bruijn graph approach to long noisy reads assembly

pacbio nanopore assembly alignment

C Updated Apr 17, 2019

philres / ngmlr

155

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference geno…

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

C++ Updated Sep 11, 2018

fritzsedlazeck / Sniffles

140

Structural variation caller using third generation sequencing

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

HTML Updated Apr 16, 2019

PacificBiosciences / blasr

93

BLASR: The PacBio® long read aligner

bioinformatics alignment long-read pacbio

C++ Updated Apr 25, 2019

PacificBiosciences / GenomicConsensus

67

PacBio® variant and consensus caller

pacbio variant-calling arrow polish consensus bioinformatics

Python Updated Apr 25, 2019

ruanjue / smartdenovo

62

Ultra-fast de novo assembler using long noisy reads

pacbio assembler

C Updated Feb 19, 2018

sequana / sequana

57

Sequana: a set of Snakemake NGS pipelines

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

Python Updated Apr 26, 2019

vpc-ccg / lordfast

28

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data

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

C Updated Mar 22, 2019

lfaino / LoReAn

27

Long Reads Annotation pipeline

annotations rna-seq pacbio nanopore

Python Updated Apr 26, 2019

PacificBiosciences / unanimity

25

Consensus library and applications

bioinformatics consensus pacbio variant-calling

C++ Updated Feb 22, 2019

PacificBiosciences / IsoSeq3

22

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

pacbio rna clustering polishing isoforms discovery

Updated Apr 5, 2019

PacificBiosciences / pbsmrtpipe

20

PacBio Workflow Engine

pipeline pbsmrtpipe pacbio

Python Updated Oct 24, 2018

PacificBiosciences / barcoding

19

Lima - Demultiplex Barcoded PacBio Samples

single-molecule barcode demultiplexing lima pacbio

R Updated Feb 25, 2019

andrewjpage / tiptoft

18

Predict plasmids from uncorrected long read data

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

Python Updated Mar 1, 2019

adigenova / fast-sg

15

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

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

C++ Updated May 29, 2018

chanzuckerberg / shasta

14

Experimental software for de novo assembly from Nanopore sequencing data.

dna sequencing assembly nanopore pacbio long-read de-novo

C++ Updated Apr 30, 2019

PacificBiosciences / minorseq

13

Minor Variant Calling and Phasing Tools

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

Updated Sep 5, 2018

dewyman / TranscriptClean

12

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

pacbio oxford-nanopore sam

Python Updated Nov 8, 2018

PacificBiosciences / smrtflow

10

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

pacbio scala swagger commandline pbsmrtpipe

Scala Updated Oct 23, 2018

bioinformatist / py3_scripts

5

Life is short, *****.

pacbio crawler scrapy blast gtf

Python Updated Jan 9, 2017

dbrowneup / Jelly2

3

A gap filling tool for genomes that utilizes PacBio long reads

genomics gap-filling pacbio

Python Updated Jan 12, 2018

bpucker / MGSE

2

Mapping-based Genome Size Estimation

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

Python Updated Apr 16, 2019

hmyh1202 / isoSeq3_test

2

A simple test report for isoSeq3 of PacificBiosciences

pacbio iso-seq isoseq-3 test

Updated Jun 1, 2018

bretonics / Bioinformatics-Software

2

Bioinformatics software list

bioinformatics software dna rna-seq sequencing single-cell analysis illumina pacbio tools

Perl Updated Jan 15, 2019

simpsonlab / preqclr

2

preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

long-read oxford-nanopore pacbio minimap2 quality bioinformatics

C++ Updated Sep 10, 2018

mbhall88 / pistis

1

Quality control plotting for long reads

nanopore oxford-nanopore bioinformatics bioinformatics-analysis plotting quality-control pacbio

Python Updated Mar 2, 2019

armintoepfer / apparatus

1

Deep learning of sequencing data

long-read neural-network tensorflow pacbio variant-calling

C++ Updated Mar 21, 2017

galantelab / sandy

1

A straightforward and complete next-generation sequencing read simulator

simulation next-generation-sequencing pacbio nanopore illumina structural-variation genomics transcriptomics

Perl Updated Mar 11, 2019

wtsi-hpag / smis

1

SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio…

genome assembly scaffolding long-reads pacbio ont oxfordnanopore

Forked from fg6/smis C Updated Feb 19, 2018

a-ludi / dentist

1

Close assembly gaps using long-reads with focus on correctness.

genome-assembly gap-filling finishing pacbio long-reads close-assembly-gaps

D Updated Jan 28, 2019

pacbio

Repositories 42