Projects in Awesome Lists tagged with long-reads

https://github.com/nextomics/nextdenovo

Fast and accurate de novo assembler for long reads

assembler genome-assembly long-reads oxford-nanopore pacbio

Last synced: 15 Dec 2024

https://github.com/goekelab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 21 Dec 2024

https://github.com/GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 13 Nov 2024

https://github.com/goekelab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

direct-rna-sequencing long-reads nanopore rna-seq transcriptomics

Last synced: 15 Dec 2024

https://github.com/mehelmy/princess

long-reads methylation phasing single-nucleotide-variation structural-variation

Last synced: 17 Nov 2024

https://github.com/bcgsc/straglr

Tandem repeat expansion detection or genotyping from long-read alignments

bioinformatics genomics long-reads tandem-repeats

Last synced: 18 Dec 2024

https://github.com/bcgsc/links

⛓ Long Interval Nucleotide K-mer Scaffolder

bloom-filter draft-assembly extract-kmer-pairs genome-assemblies long-reads scaffold scaffold-layout

Last synced: 09 Nov 2024

https://github.com/natir/yacrd

Yet Another Chimeric Read Detector

bioinformatics chimera long-reads sequence

Last synced: 18 Nov 2024

https://github.com/muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

bioinformatics bioinformatics-algorithms bioinformatics-tool classification dna-sequences fasta fastq genome genomic-data-analysis long-reads metagenomes metagenomic-analysis metagenomic-classification metagenomic-data metagenomics ncbi-refseq read-mapping refseq short-read-mapper taxonomy

Last synced: 19 Dec 2024

https://github.com/smehringer/sviper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

correction decode-genetics genetics long-reads seqan structural-variation

Last synced: 28 Oct 2024

https://github.com/bcgsc/ntlink

Minimizer-based assembly scaffolding and mapping using long reads

assembly bioinformatics long-reads minimizers scaffolding

Last synced: 09 Nov 2024

https://github.com/algbio/GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

long-reads pangenomics read-aligners variation-graph

Last synced: 16 Nov 2024

https://github.com/lpryszcz/pyscaf

Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.

genome long-reads reference scaffolding synteny

Last synced: 19 Dec 2024

https://github.com/fritzsedlazeck/svcollector

Method to optimally select samples for validation and resequencing

bioinformatics long-reads ngs ngstools structural-variation vcf

Last synced: 12 Oct 2024

https://github.com/at-cg/minichain

Long-read aligner to pangenome graphs

alignment long-reads pangenomics

Last synced: 16 Nov 2024

https://github.com/natir/rustyread

A long read simulator based on badread idea

bioinformatics long-reads

Last synced: 13 Oct 2024

https://github.com/anuradhawick/metabcc-lr

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition

binning c-plus-plus genomics long-reads metagenomics python

Last synced: 01 Nov 2024

https://github.com/tobiasrausch/lorax

A long-read analysis toolbox for cancer and population genomics

amplicon bioinformatics cancer-genomics genomics long-read-sequencing long-reads telomere

Last synced: 14 Oct 2024

https://github.com/bioinfologics/Pseudoseq.jl

Fake genomes, fake sequencing, real insights.

dna-assembly dna-sequences dna-sequencing genome-assembly linked-reads long-reads paired-end simulation simulator

Last synced: 25 Oct 2024

https://github.com/goekelab/nanoporernaseq

Nanopore RNASeq data

bioconductor long-reads nanopore r rna-seq sg-nex

Last synced: 09 Nov 2024

https://github.com/natir/knot

KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.

assembly graph long-reads

Last synced: 22 Nov 2024

https://github.com/nschan/nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

annotation arabidopsis arabidopsis-thaliana genome genome-assembly genome-sequencing hifi long-read-sequencing long-reads nanopore nextflow nextflow-pipeline nextflow-pipelines oxford-nanopore pacbio pacbio-hifi-sequencing-reads scaffolding

Last synced: 06 Nov 2024