long-read

There are 1 repository under long-read topic.

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
next-generation-sequencing pacbio oxford-nanopore mapper structural-variations long-read alignment bioconda docker
Language:C++ 284
chanzuckerberg / shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
dna sequencing assembly nanopore pacbio long-read de-novo
Language:C++ 269
marbl / SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
scaffold assembly hic long-read
Language:Python 171
kcleal / dysgu
Toolkit for calling structural variants using short or long reads
genomics bioinformatics structural-variation variant-calling paired-end long-read structural variant
Language:Cython 85
swan_vis
mortazavilab / swan_vis
A Python library to visualize and analyze long-read transcriptomes
bioinformatics transcriptome pacbio pacbio-iso-seq oxford-nanopore long-read
Language:Jupyter Notebook 48
PASSIONLab / BELLA
BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
overlapper genome-alignment pacbio-aligner longread-aligner long-read read-aligners matrix-multiplication spgemm
Language:C++ 47
vpc-ccg / lordfast
Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.
long-read mapping single-molecule-sequencing pacbio oxford-nanopore
Language:C 41
jteutenberg / downpore
Suite of tools for use in genome assembly and consensus. Work in progress.
genome-assembly long-read genome-scaffolding genome-mapping
Language:Go 31
fairliereese / LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
single-cell long-read transcriptome rna-seq demultiplexing
Language:Python 16
JensUweUlrich / Taxor
Fast and space-efficient taxonomic classification of long reads
kmer long-read long-read-sequencing metagenomics syncmer taxonomic-classification taxonomic-profiling bioinf em-algorithm pseudo-alignment xor-filter interleaved-xor-filter bioinformatics microbiome refseq taxonomy
Language:C++ 15
PacificBiosciences / minorseq
Minor Variant Calling and Phasing Tools
minor-variant haplotypes phasing drug-resistance statistics next-generation-sequencing long-read pacbio
15
guigolab / tmerge
Merge transcriptome read-to-genome alignments into non-redundant transcript models
merge bioinformatics long-read sequencing genome genomics transcriptomics transcriptome
Language:Perl 10
simpsonlab / preqclr
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
Language:C++ 4
TF-Chan-Lab / LAFITE
tool for long read transcriptome assembly
nanopore direct-rna-sequencing long-read transcriptome-assembly
Language:Jupyter Notebook 3
cihanerkut / shanti
Shallow Nanopore Sequencing for Transcriptomics
nanopore rna-seq long-read cancer
Language:Nextflow 2
shinichinamba / MuSTA
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
long-read transcriptome transcriptome-assembly isoseq-3 multi-samples
Language:Shell 2
shinichinamba / simlady
SIMulator for Long read transcriptome Analysis with RNA DecaY model
simulator long-read transcriptome isoseq-3
Language:Python 2
WEHIGenomicsRnD / nanopore-transfer-automation
Performs archiving and transfer of Nanopore sequencing data
archiving automation long-read minion nanopore promethion sequencing transfer
Language:Python 2
jib-collective / doc-mongolia
A web-documentary about uranium mining in Mongolia and it's consequences for the nomads, living there.
interactive journalism long-read mongolia scrollytelling uranium-mining
Language:HTML 0
liviuspenter / ONT-lineage-tracing
Analyses of Penter, Borji & Nagler et al., 2023
aml genotyping lineage-tracing long-read nanoranger ont scrna-seq
Language:R 0
shaniAmare / long_read_benchmark_project_scripts
A safe place for the personal scripts used in the long-read benchmarking project.
long-read
Language:Shell 0

long-read

philres / ngmlr

chanzuckerberg / shasta

marbl / SALSA

kcleal / dysgu

mortazavilab / swan_vis

PASSIONLab / BELLA

vpc-ccg / lordfast

jteutenberg / downpore

fairliereese / LR-splitpipe

JensUweUlrich / Taxor

PacificBiosciences / minorseq

guigolab / tmerge

simpsonlab / preqclr

TF-Chan-Lab / LAFITE

cihanerkut / shanti

shinichinamba / MuSTA

shinichinamba / simlady

WEHIGenomicsRnD / nanopore-transfer-automation

jib-collective / doc-mongolia

liviuspenter / ONT-lineage-tracing

shaniAmare / long_read_benchmark_project_scripts