48 results found Sort:

fritzsedlazeck
Sniffles fritzsedlazeck
95
566
other
26
Structural variation caller using third generation sequencing
ngm-lr pacbio bioconda nanopore bioinformatics structural-variation structural-variations
Created 2015-10-25
403 commits to master branch, last one 5 days ago
nanoporetech
dorado nanoporetech
68
559
other
31
Oxford Nanopore's Basecaller
genomics libtorch nanopore basecalling
Created 2022-05-17
7,037 commits to release-v0.9 branch, last one 4 days ago
ruanjue
wtdbg2 ruanjue
95
514
gpl-3.0
30
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 4 years ago
nanoporetech
medaka nanoporetech
76
430
other
48
Sequence correction provided by ONT Research
medaka nanopore
Created 2017-06-07
1,461 commits to master branch, last one 2 months ago
nanoporetech
bonito nanoporetech
123
401
other
34
A PyTorch Basecaller for Oxford Nanopore Reads
pytorch nanopore basecalling
Created 2019-11-19
1,095 commits to master branch, last one 6 months ago
a-slide
pycoQC a-slide
41
273
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
This repository has been archived (exclude archived)
Created 2017-06-16
433 commits to master branch, last one 2 months ago
marbl
Winnowmap marbl
23
266
other
15
Long read / genome alignment software
pacbio nanopore genome-analysis
Created 2020-02-11
989 commits to master branch, last one about a month ago
HKU-BAL
Clair3 HKU-BAL
30
250
unknown
11
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
601 commits to main branch, last one 9 days ago
kishwarshafin
pepper kishwarshafin
42
244
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 2 years ago
GoekeLab
awesome-nanopore GoekeLab
46
242
mit
19
A curated list of awesome nanopore analysis tools.
nanopore awesome-list bioinformatics machine-learning
Created 2021-08-17
36 commits to main branch, last one 4 months ago
nf-core
mag nf-core
111
219
mit
161
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
2,527 commits to master branch, last one 2 days ago
igordot
genomics igordot
54
201
unknown
7
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
118 commits to master branch, last one about a month ago
GoekeLab
bambu GoekeLab
24
192
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
2,159 commits to devel branch, last one about a month ago
nf-core
nanoseq nf-core
82
185
mit
139
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
Genetalks
gtz Genetalks
39
171
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
nanoporetech
remora nanoporetech
21
161
other
20
Methylation/modified base calling separated from basecalling.
nanopore basecalling methylation
Created 2021-11-22
589 commits to master branch, last one 3 months ago
nanoporetech
modkit nanoporetech
8
158
other
13
A bioinformatics tool for working with modified bases
nanopore methylation modified-bases
Created 2023-03-03
702 commits to master branch, last one 21 hours ago
ablab
IsoQuant ablab
14
154
other
13
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
ngs pacbio rna-seq nanopore bioinformatics transcriptomics
Created 2020-04-15
1,398 commits to master branch, last one 19 days ago
GoekeLab
xpore GoekeLab
23
139
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 about a year ago
nanoporetech
pod5-file-format nanoporetech
19
139
other
26
Pod5: a high performance file format for nanopore reads.
nanopore file-format apache-arrow
Created 2022-05-04
769 commits to master branch, last one 26 days ago
nf-core
taxprofiler nf-core
37
132
mit
155
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
2,031 commits to master branch, last one 23 days ago
nf-core
viralrecon nf-core
113
128
mit
107
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
Psy-Fer
SquiggleKit Psy-Fer
23
122
mit
13
SquiggleKit: A toolkit for manipulating nanopore signal data
nanopore bioinformatics
Created 2018-11-21
86 commits to master branch, last one 10 months ago
novoalab
EpiNano novoalab
31
113
gpl-2.0
6
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
417 commits to master branch, last one 5 months ago
GoekeLab
sg-nex-data GoekeLab
25
111
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
300 commits to master branch, last one 22 days ago
nanoporetech
rerio nanoporetech
10
103
other
34
Research release basecalling models and configurations
nanopore basecalling
Created 2020-03-18
143 commits to master branch, last one 6 months ago
parklab
xTea parklab
23
102
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
giesselmann
nanopype giesselmann
15
88
mit
6
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 3 years ago
khyox
recentrifuge khyox
7
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
329 commits to master branch, last one 2 months ago
adigenova
wengan adigenova
14
84
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 4 years ago