GitHub topics: long-read
kcleal/dysgu
Toolkit for calling structural variants using short or long reads
Language: Cython - Size: 46.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 102 - Forks: 13
zouyinstein/hifisr
HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).
Language: Python - Size: 84.1 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 7 - Forks: 1
guigolab/tmerge
Merge transcriptome read-to-genome alignments into non-redundant transcript models
Language: Perl - Size: 1.16 MB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 16 - Forks: 3
philres/ngmlr
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
Language: C++ - Size: 35.4 MB - Last synced at: 12 days ago - Pushed at: about 1 year ago - Stars: 297 - Forks: 40
WEHIGenomicsRnD/nanopore-transfer-automation
Performs archiving and transfer of Nanopore sequencing data
Language: Python - Size: 171 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1
nf-core/pacvar
Longread PacBio sequencing processing for WGS and PureTarget
Language: Nextflow - Size: 345 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 6
Clinical-Genomics/stranger
Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
Language: Python - Size: 354 KB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 32 - Forks: 6
JensUweUlrich/Taxor
Fast and space-efficient taxonomic classification of long reads
Language: C++ - Size: 715 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 43 - Forks: 2
huangnengCSU/longcallR-nn
longcallR_nn is a variant caller specifically designed for long-read RNA-seq data, utilizing a ResNet50 model.
Language: Rust - Size: 377 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0
chanzuckerberg/shasta 📦
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Language: C++ - Size: 11.2 MB - Last synced at: 27 days ago - Pushed at: over 2 years ago - Stars: 272 - Forks: 58
liviuspenter/ONT-lineage-tracing
Analyses of Penter, Borji & Nagler et al., Nature Communications 2024
Language: R - Size: 60.4 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
smail-lab-cmh/ga4k-sv-finder
Long read structural variants in rare disease cohort
Language: Python - Size: 47.3 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 0
mortazavilab/swan_vis
A Python library to visualize and analyze long-read transcriptomes
Language: Jupyter Notebook - Size: 63.8 MB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 54 - Forks: 11
PacificBiosciences/minorseq 📦
Minor Variant Calling and Phasing Tools
Size: 1.96 MB - Last synced at: 10 months ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 6
jteutenberg/downpore
Suite of tools for use in genome assembly and consensus. Work in progress.
Language: Go - Size: 332 KB - Last synced at: 10 months ago - Pushed at: about 4 years ago - Stars: 31 - Forks: 0
marbl/SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
Language: Python - Size: 431 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 172 - Forks: 47
shinichinamba/simlady
SIMulator for Long read transcriptome Analysis with RNA DecaY model
Language: Python - Size: 17.6 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
fairliereese/LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
Language: Python - Size: 4.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 3
vpc-ccg/lordfast
Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.
Language: C - Size: 547 KB - Last synced at: 6 months ago - Pushed at: almost 6 years ago - Stars: 41 - Forks: 4
TF-Chan-Lab/LAFITE
tool for long read transcriptome assembly
Language: Jupyter Notebook - Size: 46.5 MB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1
PASSIONLab/BELLA
BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
Language: C++ - Size: 136 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 44 - Forks: 8
shinichinamba/MuSTA
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
Language: Shell - Size: 1.54 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 2
cihanerkut/shanti
Shallow Nanopore Sequencing for Transcriptomics
Language: Nextflow - Size: 22.5 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
simpsonlab/preqclr
preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.
Language: C++ - Size: 13.2 MB - Last synced at: 7 months ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 2
shaniAmare/long_read_benchmark_project_scripts
A safe place for the personal scripts used in the long-read benchmarking project.
Language: Shell - Size: 4.7 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
jib-collective/doc-mongolia
A web-documentary about uranium mining in Mongolia and it's consequences for the nomads, living there.
Language: HTML - Size: 130 MB - Last synced at: 12 months ago - Pushed at: almost 10 years ago - Stars: 0 - Forks: 0
