pypi.org "nanopore" keyword
View the packages on the pypi.org package registry that are tagged with the "nanopore" keyword.
xron 1.0.7
A deep neural network basecaller for nanopore sequencing.10 versions - Latest release: over 1 year ago - 242 downloads last month - 21 stars on GitHub - 1 maintainer
pistis 0.3.4
Quality control plotting for long reads11 versions - Latest release: about 4 years ago - 1 dependent repositories - 244 downloads last month - 10 stars on GitHub - 1 maintainer
smftools 0.1.3
Single Molecule Footprinting Analysis in Python.3 versions - Latest release: 6 months ago - 155 downloads last month - 0 stars on GitHub - 1 maintainer
mkr-format 0.0.13
Python bindings for the MKR file format4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 443 downloads last month - 1 maintainer
Top 6.7% on pypi.org
19 versions - Latest release: 5 days ago - 1 dependent package - 3 dependent repositories - 1.97 thousand downloads last month - 584 stars on GitHub - 3 maintainers
sniffles 2.6.2
A fast structural variation caller for long-read sequencing data19 versions - Latest release: 5 days ago - 1 dependent package - 3 dependent repositories - 1.97 thousand downloads last month - 584 stars on GitHub - 3 maintainers
pynanolab 3.0.3
A data analysis and visualization software4 versions - Latest release: over 1 year ago - 188 downloads last month - 10 stars on GitHub - 1 maintainer
dajin2 0.6.1
One-step genotyping tools for targeted long-read sequencing56 versions - Latest release: about 1 month ago - 1.15 thousand downloads last month - 11 stars on GitHub - 1 maintainer
acidoseq 1.3.7
Studying Acidobacteria reads10 versions - Latest release: over 6 years ago - 1 dependent repositories - 393 downloads last month - 0 stars on GitHub - 1 maintainer
minfq 1.4.7
Command line interface for uploading fastq files and monitoring minKNOW for minotour.27 versions - Latest release: about 3 years ago - 1 dependent repositories - 895 downloads last month - 10 stars on GitHub - 3 maintainers
squigualiser 0.6.3
Visualise ONT raw signals10 versions - Latest release: 12 months ago - 1 dependent package - 177 downloads last month - 95 stars on GitHub - 1 maintainer
Top 6.0% on pypi.org
91 versions - Latest release: 6 months ago - 3 dependent repositories - 3.86 thousand downloads last month - 447 stars on GitHub - 1 maintainer
medaka 2.0.1
Neural network sequence error correction.91 versions - Latest release: 6 months ago - 3 dependent repositories - 3.86 thousand downloads last month - 447 stars on GitHub - 1 maintainer
medaka-cpu 2.0.1
Neural network sequence error correction.45 versions - Latest release: 6 months ago - 1 dependent repositories - 1.9 thousand downloads last month - 447 stars on GitHub - 1 maintainer
ampligone 2.0.1
AmpliGone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon...11 versions - Latest release: 18 days ago - 437 downloads last month - 16 stars on GitHub - 3 maintainers
poreplex 0.4.1
A versatile sequence read processor for nanopore direct RNA sequencing7 versions - Latest release: about 6 years ago - 1 dependent repositories - 336 downloads last month - 79 stars on GitHub - 1 maintainer
nanocompore 1.0.4
Software package that identifies raw signal changes between two conditions from https://github.co...6 versions - Latest release: almost 4 years ago - 1 dependent repositories - 231 downloads last month - 82 stars on GitHub - 1 maintainer
pyslow5 1.3.0
slow5lib python bindings16 versions - Latest release: 7 months ago - 4 dependent packages - 1 dependent repositories - 1.31 thousand downloads last month - 35 stars on GitHub - 2 maintainers
nanoraw 0.4.2
Analysis of nanopore sequencing data.8 versions - Latest release: over 1 year ago - 1 dependent repositories - 185 downloads last month - 46 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
14 versions - Latest release: over 1 year ago - 3 dependent packages - 4 dependent repositories - 5.52 thousand downloads last month - 20 stars on GitHub - 2 maintainers
pyspoa 0.2.1
Python bindings to spoa14 versions - Latest release: over 1 year ago - 3 dependent packages - 4 dependent repositories - 5.52 thousand downloads last month - 20 stars on GitHub - 2 maintainers
tbpore 0.7.1
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data12 versions - Latest release: 10 months ago - 1 dependent repositories - 181 downloads last month - 11 stars on GitHub - 1 maintainer
xpore 0.5.6
xpore is a python package for Nanopore data analysis of differential RNA modifications.11 versions - Latest release: over 4 years ago - 1 dependent repositories - 381 downloads last month - 147 stars on GitHub - 1 maintainer
fast5seek 0.1.1
Get paths for fast5 files contained in BAM, SAM, or fastq.2 versions - Latest release: over 6 years ago - 1 dependent repositories - 71 downloads last month - 12 stars on GitHub - 1 maintainer
pepper-polish 0.1.5
RNN based standalone assembly polisher.8 versions - Latest release: over 4 years ago - 1 dependent repositories - 289 downloads last month - 245 stars on GitHub - 1 maintainer
lafite 1.0.2
Nanopore Direct RNA-seq Transcriptome Assembly4 versions - Latest release: over 2 years ago - 1 dependent repositories - 87 downloads last month - 3 stars on GitHub - 1 maintainer
bio-anglerfish 0.7.0
Anglerfish, a tool to demultiplex Illumina libraries from ONT data7 versions - Latest release: 8 months ago - 1 dependent repositories - 212 downloads last month - 2 stars on GitHub - 1 maintainer
deepchopper-cli 1.2.6
CLI for DeepChopper: A Genomic Language Model for Chimera Artifact Detection7 versions - Latest release: 5 months ago - 2.14 thousand downloads last month - 3 stars on GitHub - 1 maintainer
deepchopper 1.2.6
A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing7 versions - Latest release: 5 months ago - 883 downloads last month - 3 stars on GitHub - 1 maintainer
Top 8.9% on pypi.org
51 versions - Latest release: 8 days ago - 1 dependent repositories - 1.28 thousand downloads last month - 404 stars on GitHub - 1 maintainer
ont-bonito 0.9.0
A PyTorch Basecaller for Oxford Nanopore Reads51 versions - Latest release: 8 days ago - 1 dependent repositories - 1.28 thousand downloads last month - 404 stars on GitHub - 1 maintainer
tiptoft 1.0.2
tiptoft: predict which plasmid should be present from uncorrected long read data6 versions - Latest release: over 5 years ago - 1 dependent repositories - 243 downloads last month - 39 stars on GitHub - 1 maintainer
pycoqc 2.5.2
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies seque...50 versions - Latest release: over 4 years ago - 1.99 thousand downloads last month - 242 stars on GitHub - 1 maintainer
taeper 0.1.0
Simulate repeating a nanopore experiment.1 version - Latest release: about 7 years ago - 1 dependent repositories - 51 downloads last month - 19 stars on GitHub - 1 maintainer
chiron 0.6.1
A deep neural network basecaller for nanopore sequencing.14 versions - Latest release: over 5 years ago - 353 downloads last month - 122 stars on GitHub - 1 maintainer
sequali 0.12.0
Sequali is a QC tool that generates useful graphs for both short and long-read data.17 versions - Latest release: 6 months ago - 5.04 thousand downloads last month - 0 stars on GitHub - 1 maintainer
variantbreak 1.0.4
Structural variant analyzer for data visualization on VariantMap2 versions - Latest release: over 4 years ago - 1 dependent repositories - 39 downloads last month - 3 stars on GitHub - 1 maintainer
nanostat 1.6.0
Calculate statistics for Oxford Nanopore sequencing data and alignments28 versions - Latest release: over 3 years ago - 2 dependent repositories - 727 downloads last month - 78 stars on GitHub - 1 maintainer
fast5purge 0.2.0
Remove sensible content from a fast5 file or directory4 versions - Latest release: over 6 years ago - 1 dependent repositories - 88 downloads last month - 2 stars on GitHub - 1 maintainer
surpyvor 0.15.0
Manipulate vcf files of structural variants using SURVIVOR10 versions - Latest release: almost 2 years ago - 1 dependent repositories - 185 downloads last month - 18 stars on GitHub - 1 maintainer
Top 9.3% on pypi.org
34 versions - Latest release: about 4 years ago - 2 dependent repositories - 1.26 thousand downloads last month - 201 stars on GitHub - 1 maintainer
nanofilt 2.8.0
Filtering and trimming of Oxford Nanopore Sequencing data34 versions - Latest release: about 4 years ago - 2 dependent repositories - 1.26 thousand downloads last month - 201 stars on GitHub - 1 maintainer
Top 6.9% on pypi.org
155 versions - Latest release: 3 months ago - 3 dependent repositories - 5.15 thousand downloads last month - 461 stars on GitHub - 1 maintainer
nanoplot 1.44.1
Plotting suite for Oxford Nanopore sequencing data and alignments155 versions - Latest release: 3 months ago - 3 dependent repositories - 5.15 thousand downloads last month - 461 stars on GitHub - 1 maintainer
nanocomp 1.25.2
Comparing runs of Oxford Nanopore sequencing data and alignments74 versions - Latest release: 17 days ago - 1.77 thousand downloads last month - 125 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
70 versions - Latest release: over 1 year ago - 1 dependent package - 13 dependent repositories - 2.77 thousand downloads last month - 11 stars on GitHub - 1 maintainer
nanoget 1.19.3
Functions to extract information from Oxford Nanopore sequencing data and alignments.70 versions - Latest release: over 1 year ago - 1 dependent package - 13 dependent repositories - 2.77 thousand downloads last month - 11 stars on GitHub - 1 maintainer
nanopack 1.1.0
Install all Oxford Nanopore scrips and modules for processing and analysis9 versions - Latest release: almost 5 years ago - 1 dependent repositories - 243 downloads last month - 236 stars on GitHub - 1 maintainer
nanosplit 0.1.4
Perform splitting of Oxford Nanopore sequencing data in a fail and pass dataset.5 versions - Latest release: over 7 years ago - 1 dependent repositories - 122 downloads last month - 1 stars on GitHub - 1 maintainer
nanoqc 0.10.0
Create fastQC-like plots for Oxford Nanopore sequencing data18 versions - Latest release: 6 months ago - 1 dependent repositories - 418 downloads last month - 102 stars on GitHub - 1 maintainer
methplotlib 0.21.2
Plot methylation data obtained from nanopolish18 versions - Latest release: 11 months ago - 1 dependent repositories - 334 downloads last month - 92 stars on GitHub - 1 maintainer
fastq-anonymous 1.0.1
Change the sequence of a fastq file to enable sharing of confidential information, for troublesho...2 versions - Latest release: over 7 years ago - 1 dependent repositories - 48 downloads last month - 0 stars on GitHub - 1 maintainer
imgtools 0.2.0
Some tools for manipulating image files2 versions - Latest release: about 7 years ago - 1 dependent repositories - 131 downloads last month - 1 stars on GitHub - 1 maintainer
nanolyse 1.2.1
Removing reads mapping to the lambda genome18 versions - Latest release: over 2 years ago - 1 dependent repositories - 480 downloads last month - 29 stars on GitHub - 1 maintainer
hairloom 0.1.1
A package to analyze split reads of long read data11 versions - Latest release: 16 days ago - 473 downloads last month - 0 stars on GitHub - 1 maintainer
pod5-format-tools 0.0.41
Tools for use with the POD5 file format9 versions - Latest release: over 2 years ago - 2 dependent repositories - 175 downloads last month - 146 stars on GitHub - 1 maintainer
Top 4.5% on pypi.org
27 versions - Latest release: 5 months ago - 7 dependent packages - 2 dependent repositories - 11 thousand downloads last month - 146 stars on GitHub - 1 maintainer
pod5 0.3.23
Oxford Nanopore Technologies Pod5 File Format Python API and Tools27 versions - Latest release: 5 months ago - 7 dependent packages - 2 dependent repositories - 11 thousand downloads last month - 146 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
27 versions - Latest release: 5 months ago - 1 dependent package - 1 dependent repositories - 18.6 thousand downloads last month - 146 stars on GitHub - 1 maintainer
lib-pod5 0.3.23
Python bindings for the POD5 file format27 versions - Latest release: 5 months ago - 1 dependent package - 1 dependent repositories - 18.6 thousand downloads last month - 146 stars on GitHub - 1 maintainer
Top 9.1% on pypi.org
10 versions - Latest release: over 2 years ago - 1 dependent package - 2 dependent repositories - 1.7 thousand downloads last month - 146 stars on GitHub - 1 maintainer
pod5-format 0.0.41
Python bindings for the POD5 file format10 versions - Latest release: over 2 years ago - 1 dependent package - 2 dependent repositories - 1.7 thousand downloads last month - 146 stars on GitHub - 1 maintainer
nanovar 1.8.3
Structural variant caller using low-depth long reads28 versions - Latest release: 3 months ago - 1 dependent repositories - 560 downloads last month - 31 stars on GitHub - 1 maintainer
ont-bonito-cuda113 0.5.3
A PyTorch Basecaller for Oxford Nanopore Reads6 versions - Latest release: almost 3 years ago - 1 dependent repositories - 124 downloads last month - 404 stars on GitHub - 1 maintainer
ont-bonito-cuda111 0.5.3
A PyTorch Basecaller for Oxford Nanopore Reads11 versions - Latest release: almost 3 years ago - 1 dependent repositories - 225 downloads last month - 404 stars on GitHub - 1 maintainer
nanogo-basecaller 0.1.6
A bioinformatics pipeline for basecalling ONT NGS Data.7 versions - Latest release: 12 days ago - 684 downloads last month - 1 maintainer
Top 7.8% on pypi.org
17 versions - Latest release: 7 months ago - 3 dependent repositories - 720 downloads last month - 168 stars on GitHub - 1 maintainer
ont-remora 3.3.0
Nanopore methylation/modified base calling detached from basecalling17 versions - Latest release: 7 months ago - 3 dependent repositories - 720 downloads last month - 168 stars on GitHub - 1 maintainer
pyguppyclient 0.1.0
Python client library for Guppy11 versions - Latest release: almost 4 years ago - 1 dependent package - 1 dependent repositories - 253 downloads last month - 31 stars on GitHub - 1 maintainer
Top 7.5% on pypi.org
2 versions - Latest release: over 2 years ago - 4 dependent packages - 1 dependent repositories - 11.6 thousand downloads last month - 40 stars on GitHub - 1 maintainer
vbz-h5py-plugin 1.0.1
Oxford Nanopore Technologies VBZ HDF plugin for h5py2 versions - Latest release: over 2 years ago - 4 dependent packages - 1 dependent repositories - 11.6 thousand downloads last month - 40 stars on GitHub - 1 maintainer
Top 3.8% on pypi.org
37 versions - Latest release: about 1 year ago - 9 dependent packages - 26 dependent repositories - 9.1 thousand downloads last month - 142 stars on GitHub - 1 maintainer
ont-fast5-api 4.1.3
Oxford Nanopore Technologies fast5 API software37 versions - Latest release: about 1 year ago - 9 dependent packages - 26 dependent repositories - 9.1 thousand downloads last month - 142 stars on GitHub - 1 maintainer
ont-tombo 1.5.1
Analysis of raw nanopore sequencing data.12 versions - Latest release: about 5 years ago - 1 dependent repositories - 389 downloads last month - 233 stars on GitHub - 1 maintainer
recentrifuge 1.16.0
Robust comparative analysis and contamination removal for metagenomics86 versions - Latest release: about 1 month ago - 1 dependent repositories - 2.37 thousand downloads last month - 89 stars on GitHub - 1 maintainer
blue-crab 0.3.0
blue-crab: A Slow5/Blow5 <-> Pod5 converter4 versions - Latest release: 3 months ago - 216 downloads last month - 38 stars on GitHub - 2 maintainers
pacu-snp 0.0.7
Workflow for whole genome sequencing based phylogeny of Illumina and ONT data.6 versions - Latest release: 3 months ago - 210 downloads last month - 5 stars on GitHub - 1 maintainer
deepsignal2 0.1.3
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 111 downloads last month - 28 stars on GitHub - 1 maintainer
plasmidpredictor 0.1.0
plasmidpredictor: predict which plasmid should be present from uncorrected long read data1 version - Latest release: over 6 years ago - 1 dependent repositories - 59 downloads last month - 39 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
48 versions - Latest release: 10 months ago - 1 dependent package - 13 dependent repositories - 1.09 thousand downloads last month - 9 stars on GitHub - 1 maintainer
nanomath 1.4.0
A few simple math function for other Oxford Nanopore processing scripts48 versions - Latest release: 10 months ago - 1 dependent package - 13 dependent repositories - 1.09 thousand downloads last month - 9 stars on GitHub - 1 maintainer
sequana-lora 1.0.0
Run assembler (Canu, Flye, Hifiasm) on a set of long read files1 version - Latest release: 18 days ago
ont-guppy-duplex-pipeline 1.0.3
Oxford Nanopore Technologies duplex pipeline scripts for guppy4 versions - Latest release: over 2 years ago - 1 dependent repositories - 71 downloads last month - 1 maintainer
mccloud-cli 0.0.8
A command line to assist McCloud users.8 versions - Latest release: over 3 years ago - 1 dependent repositories - 216 downloads last month - 272 stars on GitHub - 2 maintainers
fastqmetrics 0.1.0
Het hoeft voor1 version - Latest release: over 7 years ago - 1 dependent repositories - 32 downloads last month - 0 stars on GitHub - 1 maintainer
mosaic-nist 1.3.5
A Modular Single-Molecule Analysis Interface.16 versions - Latest release: over 7 years ago - 2 dependent repositories - 297 downloads last month - 38 stars on GitHub - 1 maintainer
mkr-format-tools 0.0.13
Tools for use with the MKR file format4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 65 downloads last month - 1 maintainer
trackcluster 0.1.7
RNA-seq analysis for Long read RNA sequencing6 versions - Latest release: 6 months ago - 251 downloads last month - 12 stars on GitHub - 1 maintainer
nanoplotter 1.10.0
Plotting functions of Oxford Nanopore sequencing data99 versions - Latest release: almost 6 years ago - 1 dependent package - 2 dependent repositories - 1.32 thousand downloads last month - 2 stars on GitHub - 1 maintainer
picopore 1.2.0
A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.21 versions - Latest release: over 7 years ago - 1 dependent repositories - 169 downloads last month - 31 stars on GitHub - 1 maintainer
nanomix 0.2.0
Methods for cell type deconvolution from Oxford Nanopore methylation calling3 versions - Latest release: almost 2 years ago - 129 downloads last month - 11 stars on GitHub - 1 maintainer
nanosim-h 1.1.0.4
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.5 versions - Latest release: over 6 years ago - 1 dependent repositories - 114 downloads last month - 17 stars on GitHub - 1 maintainer
comptg2 0.2.0
Telomeric allele scoring tool for output from Telogator2.3 versions - Latest release: 6 months ago - 134 downloads last month - 14 stars on GitHub - 1 maintainer
deepsignal 0.2.0
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads11 versions - Latest release: about 3 years ago - 1 dependent repositories - 222 downloads last month - 112 stars on GitHub - 1 maintainer
deepsignal-plant 0.1.6
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads ...7 versions - Latest release: almost 3 years ago - 1 dependent repositories - 217 downloads last month - 57 stars on GitHub - 1 maintainer
pod5viewer 1.1.2
GUI for inspecting ONT pod5 files6 versions - Latest release: 4 months ago - 200 downloads last month - 4 stars on GitHub - 1 maintainer
methylink 0.6.0
methylink is a tool to link methylation tags between SAM/BAM files.6 versions - Latest release: over 1 year ago - 161 downloads last month - 1 stars on GitHub - 1 maintainer
seamlessf5 0.2
Helpers for smoother transitioning to multi-read FAST5 files2 versions - Latest release: over 6 years ago - 1 dependent repositories - 57 downloads last month - 6 stars on GitHub - 1 maintainer
nanosv 1.2.4
Structural variation detection tool for Oxford Nanopore data.12 versions - Latest release: over 5 years ago - 1 dependent repositories - 202 downloads last month - 86 stars on GitHub - 1 maintainer
lrplots 0.7.0
Plot collection for Long Read Sequencing8 versions - Latest release: about 2 years ago - 1 dependent repositories - 166 downloads last month - 12 stars on GitHub - 1 maintainer
strainy 1.4 removed
Metagenomic strain phasing and assmebly using long reads4 versions - Latest release: 8 months ago - 41 stars on GitHub
Related Keywords
sequencing
22
bioinformatics
21
plotting
9
quality
8
control
8
basecalling
7
python
7
pacbio
7
genomics
6
methylation
6
processing
5
nanopore-sequencing
5
fast5
5
neural network
5
pytorch
4
oxford-nanopore
4
long-read-sequencing
4
apache-arrow
4
file-format
4
long-reads
4
slow5
3
rna-seq
3
assembly
3
pod5
3
analysis
3
illumina
3
variant-calling
2
infectious-diseases
2
global-health
2
bioinformatics-pipeline
2
deep-learning
2
biology
2
rust
2
fastq
2
deep learning
2
ont
2
long-read
2
Nanopore
2
longread
2
ngs
2
metagenomics
2
epigenetics
2
hdf5
2
compression
2
guppy
2
filtering
2
trimming
2
statistics
2
long read
2
nanovar
2
sv
2
simulation
2
uncorrected
2
research
2
plasmidfinder
2
plasmid
2
pathogen
2
kmer
2
signal
2
medaka
2
python3
2
genome
2
basecaller
2
demultiplexing
2
rna-modifications
2
high-throughput
2
correction
2
machine-learning
2
structural variant caller
1
contamination-removal
1
centrifuge
1
clark
1
comparative-genomics
1
contamination
1
kraken
1
lmat
1
low-biomass
1
pistis
1
robustness
1
phylogeny
1
low coverage
1
low depth
1
ONT
1
dorado
1
NGS
1
pipeline
1
primer-trimming
1
single-locus
1
protein-dna-binding
1
h5py
1
vbz
1
chromatin-accessibility
1
anndata
1
quality-control
1
bioinformatics-analysis
1
comparative-analysis
1
metagenomic-analysis
1
hifi
1
qualitycontrol
1
plot
1