A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

k-mer based assembly evaluation

quality filtering tool for long reads

Genome assembly evaluation tool

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A versatile pairwise aligner for genomic and spliced nucleotide sequences

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Codon-Aware Multiple Sequence Alignments

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Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)

Python Script to create a histogram of the sequences lengths in a Fasta file (useful to get the distribution of Pacbio Reads for example)

R-based autopolyploid population and population genetic simulation

Python library to facilitate genome assembly, annotation, and comparative genomics

Automated and distributed population genetic model inference from allele frequency spectra

SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.

🌌 The R easystats-project

Simple Python version management

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).

Tools for the analysis of structural variation in genomes

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

Synteny and Rearrangement Identifier

Pangenome-based genome inference

A deep learning-based method to infer leaf angle variation from photographs.

EasyCodeML: A visual tool for analysis of selection using CodeML

Docker - Beginners | Intermediate | Advanced

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