All Categories → No Category → long-reads

Top 11 long-reads open source projects

Predict plasmids from uncorrected long read data

✭ 27

python TeX Dockerfile bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

Method to optimally select samples for validation and resequencing

✭ 20

C++Makefile perl r shell bioinformatics ngs vcf ngstools structural-variation long-reads

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

✭ 47

C++shell Makefile Dockerfile ngs consensus correction long msa reads contigs long-reads multiple-sequence-alignment polishing self-correction

Close assembly gaps using long-reads at high accuracy.

✭ 39

d shell python docker bioinformatics snakemake cluster singularity dub pacbio genome-assembly daligner long-reads gap-filling close-assembly-gaps damapper

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

✭ 119

python Jupyter Notebook c C++shell Dockerfile Makefile deep-learning nanopore genomics computational-biology variant-calling long-reads ont-data ont-models

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

✭ 68

C++python c Makefile bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

pipeline-structural-variation

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

✭ 104

python nanopore whole-genome-sequencing structural-variation long-reads

PEPPER-Margin-DeepVariant

✭ 179

python C++c nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing

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…

✭ 44

VHDL Verilog shell C++Cuda SystemVerilog fpga gpu smith-waterman needleman-wunsch sequence-alignment long-reads minimap2 short-reads hardware-accelerator sequence-aligner edlib pre-alignment-filtering wavefront-alignment

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

✭ 21

c C++Makefile python tandem-repeats long-reads multiple-sequence-alignment seed-and-chain partial-order-alignment

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

✭ 15

c C++Makefile python tandem-repeats long-reads multiple-sequence-alignment nanopore-sequencing seed-and-chain partial-order-alignment

1-11 of 11 long-reads projects