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mecat2

miniasm

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

minigraph

Proof-of-concept seq-to-graph mapper and graph generator

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

msprime

Simulate genealogical trees and genomic sequence data using population genetic models

mumandco

nanopolish

Signal-level algorithms for MinION data

newick_utils

shell tools for processing phylogenetic trees

nextdenovo

Fast and accurate de novo assembler for third generation sequencing (TGS) reads

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

notebook

ohana

mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.

oneliners

Useful bash one-liners for bioinformatics.

opensees

OpenSees Source Code Repository

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

paragraph

Graph realignment tools for structural variants

pasapipeline

PASA software

pb-assembly

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

pbsim2

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

pggb

the pangenome graph builder

phylotol

pilon

Pilon is an automated genome assembly improvement and variant detection tool

pipeline-nanopore-ref-isoforms

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

ploidyngs

Explore ploidy levels from NGS data alone

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

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

pychopper

cDNA read preprocessing

python-100-days

Python - 100天从新手到大师

quast

Genome assembly evaluation tool