43 results found Sort:

fritzsedlazeck
Sniffles fritzsedlazeck
86
523
other
27
Structural variation caller using third generation sequencing
ngm-lr pacbio bioconda nanopore bioinformatics structural-variation structural-variations
Created 2015-10-25
262 commits to master branch, last one about a month ago
ruanjue
wtdbg2 ruanjue
91
497
gpl-3.0
31
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
pacbio assembly nanopore alignment
Created 2017-09-29
437 commits to master branch, last one 3 years ago
nanoporetech
dorado nanoporetech
53
436
other
32
Oxford Nanopore's Basecaller
genomics libtorch nanopore basecalling
Created 2022-05-17
5,621 commits to release-v0.7 branch, last one 9 days ago
nanoporetech
medaka nanoporetech
73
391
other
46
Sequence correction provided by ONT Research
medaka nanopore
Created 2017-06-07
1,424 commits to master branch, last one about a month ago
nanoporetech
bonito nanoporetech
117
380
other
36
A PyTorch Basecaller for Oxford Nanopore Reads
pytorch nanopore basecalling
Created 2019-11-19
1,095 commits to master branch, last one 22 days ago
a-slide
pycoQC a-slide
39
247
gpl-3.0
5
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
nanopore generates-plots jupyter-notebook computing-metrics
Created 2017-06-16
432 commits to master branch, last one 7 months ago
kishwarshafin
pepper kishwarshafin
41
231
mit
10
PEPPER-Margin-DeepVariant
nanopore variants long-reads pacbio-ccs oxford-nanopore variant-calling genome-variation assembly-polishing
Created 2019-05-10
1,281 commits to r0.8 branch, last one about a year ago
marbl
Winnowmap marbl
21
229
other
15
Long read / genome alignment software
pacbio nanopore genome-analysis
Created 2020-02-11
987 commits to master branch, last one 13 days ago
HKU-BAL
Clair3 HKU-BAL
27
227
unknown
10
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
pacbio genomics illumina nanopore ont-data long-reads ont-models deep-learning variant-calling variant-detection computational-biology
Created 2021-03-30
586 commits to main branch, last one about a month ago
GoekeLab
awesome-nanopore GoekeLab
42
218
mit
17
A curated list of awesome nanopore analysis tools.
nanopore awesome-list bioinformatics machine-learning
Created 2021-08-17
34 commits to main branch, last one 7 months ago
igordot
genomics igordot
54
192
unknown
6
A collection of scripts and notes related to genomics and bioinformatics
dna gtf vcf fast5 fasta fastq science genomics illumina nanopore workflow sequencing bioinformatics
Created 2015-12-22
115 commits to master branch, last one about a year ago
nf-core
mag nf-core
102
189
mit
157
Assembly and binning of metagenomes
binning nf-core assembly nanopore nextflow pipeline workflow annotation metagenomes metagenomics bioinformatics nanopore-sequencing long-read-sequencing
Created 2018-05-22
2,180 commits to master branch, last one 16 days ago
Genetalks
gtz Genetalks
39
169
other
17
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
bam gtx sam gene fastq pacbio compress nanopore compression compression-rate fastq-compression genomic-data-compression
Created 2016-11-11
824 commits to master branch, last one 2 years ago
GoekeLab
bambu GoekeLab
22
167
gpl-3.0
7
Reference-guided transcript discovery and quantification for long read RNA-Seq data
r bambu rna-seq nanopore long-reads bioconductor transcriptomics rna-seq-analysis nanopore-sequencing transcript-quantification transcript-reconstruction
Created 2020-02-07
2,144 commits to devel branch, last one 2 months ago
nf-core
nanoseq nf-core
75
151
mit
134
Nanopore demultiplexing, QC and alignment pipeline
qc nf-core nanopore nextflow pipeline workflow alignment demultiplexing
Created 2019-09-09
1,587 commits to master branch, last one about a year ago
nanoporetech
remora nanoporetech
17
147
other
20
Methylation/modified base calling separated from basecalling.
nanopore basecalling methylation
Created 2021-11-22
571 commits to master branch, last one about a month ago
GoekeLab
xpore GoekeLab
22
131
mit
9
Identification of differential RNA modifications from nanopore direct RNA sequencing
rna python rna-seq genomics nanopore modification transcriptomics machine-learning rna-modifications nanopore-sequencing
Created 2020-01-06
367 commits to master branch, last one 7 months ago
ablab
IsoQuant ablab
11
126
other
10
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
ngs pacbio rna-seq nanopore bioinformatics transcriptomics
Created 2020-04-15
1,322 commits to master branch, last one 8 days ago
Psy-Fer
SquiggleKit Psy-Fer
22
120
mit
13
SquiggleKit: A toolkit for manipulating nanopore signal data
nanopore bioinformatics
Created 2018-11-21
86 commits to master branch, last one 4 months ago
nanoporetech
pod5-file-format nanoporetech
14
118
other
27
Pod5: a high performance file format for nanopore reads.
nanopore file-format apache-arrow
Created 2022-05-04
700 commits to master branch, last one 6 days ago
nanoporetech
modkit nanoporetech
5
116
other
14
A bioinformatics tool for working with modified bases
nanopore methylation modified-bases
Created 2023-03-03
624 commits to master branch, last one 5 days ago
nf-core
viralrecon nf-core
103
111
mit
101
Assembly and intrahost/low-frequency variant calling for viral samples
ont artic viral virus covid19 nf-core amplicon assembly covid-19 illumina nanopore nextflow pipeline workflow sars-cov-2 metagenomics oxford-nanopore variant-calling long-read-sequencing
Created 2020-03-30
2,788 commits to master branch, last one about a year ago
novoalab
EpiNano novoalab
31
107
gpl-2.0
7
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
m6a nanopore direct-rna rna-sequencing m6a-rna-modifications
Created 2018-12-19
416 commits to master branch, last one 2 months ago
nf-core
taxprofiler nf-core
32
104
mit
148
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification
Created 2022-02-18
1,784 commits to master branch, last one 6 days ago
nanoporetech
rerio nanoporetech
9
97
other
34
Research release basecalling models and configurations
nanopore basecalling
Created 2020-03-18
143 commits to master branch, last one 8 days ago
GoekeLab
sg-nex-data GoekeLab
23
94
unknown
7
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
rna-seq nanopore long-reads transcriptomics direct-rna-sequencing
Created 2019-02-28
286 commits to master branch, last one 2 months ago
giesselmann
nanopype giesselmann
15
89
mit
7
Snakemake pipelines for nanopore sequencing data archiving and processing
docker nanopore pipeline workflow singularity snakemake-pipelines
This repository has been archived (exclude archived)
Created 2018-11-12
599 commits to master branch, last one 2 years ago
parklab
xTea parklab
19
87
other
9
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
pacbio illumina nanopore linked-reads transposable-elements mobile-element-insertion
Created 2018-07-12
144 commits to master branch, last one about a year ago
khyox
recentrifuge khyox
6
86
other
6
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
ngs lmat clark kraken nanopore centrifuge robustness low-biomass metagenomics contamination comparative-genomics
Created 2017-08-01
322 commits to master branch, last one 4 months ago
adigenova
wengan adigenova
13
83
agpl-3.0
7
An accurate and ultra-fast hybrid genome assembler
hybrid pacbio illumina nanopore genome-assembler
Created 2019-03-04
50 commits to master branch, last one 3 years ago