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68 search results found

Nextdenovo ⭐ 306

Fast and accurate de novo assembler for long reads

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

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

PEPPER-Margin-DeepVariant

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

SALSA: A tool to scaffold long read assemblies with Hi-C data

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

Long Read Pipelines ⭐ 108

Long read production pipelines

Brickyeditor ⭐ 103

WYSIWYG block editor jQuery plugin.

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Sg Nex Data ⭐ 80

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

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Toolkit for calling structural variants using short or long reads

Princess ⭐ 74

⛓Long Interval Nucleotide K-mer Scaffolder

Yet Another Chimeric Read Detector

Metacache ⭐ 49

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

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

Minimap2 Rs ⭐ 46

Rust bindings to minimap2 library

Long-reads Gap-free Chromosome-scale Assembler

Sneakysnake ⭐ 44

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.

Close assembly gaps using long-reads at high accuracy.

A versatile compressor of third generation sequencing reads.

Swan_vis ⭐ 43

A Python library to visualize and analyze long-read transcriptomes

ClairS - a deep-learning method for long-read somatic small variant calling

Scalable long read self-correction and assembly polishing with multiple sequence alignment

A fast tool for hybrid genome assembly of long and short reads

Graph-based assembly phasing

Lordfast ⭐ 31

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

Downpore ⭐ 30

Suite of tools for use in genome assembly and consensus. Work in progress.

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

Tandem repeat expansion detection or genotyping from long-read alignments

Order and orientation of complete bacterial genomes

Tidehunter ⭐ 22

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Gssplayground ⭐ 21

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

Graphchainer ⭐ 20

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

Minimizer-based assembly scaffolding and mapping using long reads

Rustyread ⭐ 20

A long read simulator based on badread idea

Predict plasmids from uncorrected long read data

Minichain ⭐ 18

Long-read aligner to pangenome graphs

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

Clairs To ⭐ 18

ClairS-TO - a deep-learning method for tumor-only somatic SNV calling

Centroflye ⭐ 17

An algorithm for centromere assembly using long error-prone reads

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

Tidehunter ⭐ 17

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

A long-read analysis toolbox for cancer and population genomics

Metabcc Lr ⭐ 16

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

Minorseq ⭐ 14

Minor Variant Calling and Phasing Tools

STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio.

Edgecase ⭐ 13

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Lr Splitpipe ⭐ 13

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Fast and space-efficient taxonomic classification of long reads

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

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Longread_plots ⭐ 10

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads

Trackcluster ⭐ 9

An analysis pipeline for Nanopore direct-RNA sequencing

Derives consensus sequences from a set of long noisy reads by clustering and error correction.

Coronavirus (SARS-Cov-2) sequencing analysis

Project Diploid Assembly ⭐ 8

Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data

A scalable variant calling and benchmarking framework supporting both short and long reads.

Pseudoseq.jl ⭐ 6

Fake genomes, fake sequencing, real insights.

Svjedi Graph ⭐ 5

SV genotyper for long reads with a variation graph

Related Searches

Bioinformatics Long Reads (36)

Python Long Reads (31)

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