Jue Ruan

unialigner. C++

verkko. Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

SRY. SRY: an effective method for sorting long-read of sex-limited (Y or W) chromosome.

GAEP. A genome assembly assessment pipeline.

wtdbg2. Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

py12306. 🚂 12306 购票助手，支持集群，多账号，多任务购票以及 Web 页面管理

iGDA. Detect and phase minor SNVs from long-read sequencing data

nanoreviser. NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm

hifiasm. Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

GraphAligner. C++

minigraph. Sequence-to-graph mapper and graph generator

ksw2. Global alignment and alignment extension

parasail. Pairwise Sequence Alignment Library

Long-read-assembler-comparison. Benchmarking of long-read assembly tools for bacterial whole genomes

Peregrine. Peregrine: Fast Genome Assembler Using SHIMMER Index

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

Flye. De novo assembler for single molecule sequencing reads using repeat graphs

spoa. SIMD partial order alignment tool/library

NA12878. Data and analysis for NA12878 genome on nanopore

gtz. A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

gfa1. This repo is deprecated. Please use gfatools instead.

BlindCall. DNA base-calling using blind convolution.

minimap2. A versatile pairwise aligner for genomic and spliced nucleotide sequences

MECAT. MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

wtdbg. A fuzzy Bruijn graph approach to long noisy reads assembly

DBG2OLC. A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

minimap. This repo is DEPRECATED. Please use minimap2, the successor of minimap.

miniasm. Ultrafast de novo assembly for long noisy reads (though having no consensus step)

smartdenovo. Ultra-fast de novo assembler using long noisy reads