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hisat2

Graph-based alignment (Hierarchical Graph FM index)

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

kasptree

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

kmersgwas

A library for running k-mers based GWAS

kwip

De novo estimates of genetic relatedness from next-gen sequencing data

l_rna_scaffolder

Use long transcriptome reads to scaffold genomes

last-genome-alignments

lrsim

10x Genomics Reads Simulator

ltsm-stock-predictor

Predicting different stock prices using Long Short-Term Memory Recurrent Neural Network in Python using TensorFlow 2 and Keras.

maize_v4_te_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

maker2_pm_genome_annotation

Using MAKER2 FOR ANNOTATION OF FOUR DICOT PM genomes

masurca

mcscan

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

mcscanx

MCScanX: Multiple Collinearity Scan toolkit X version. The most frequently used synteny analysis tool in the world!

mec

Contig Misassembly Correction

mec-1

Evaluating MEC

medusa

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

metapgn

A pipeline for construction and graphical visualization of annotated pangenome networks.

mummer

Mummer alignment tool

nanoplot

Plotting scripts for long read sequencing data

ncbi_blast_tutorial

Short introduction to command line NCBI blast tools

ncbitax2lin

Convert NCBI taxonomy dump into lineages

nematoda-te-evolution

Analysis for the paper "Genetic drift, not life history or RNAi, determine long term evolution of transposable elements"

nextpolish

Fast and accurately polish the genome generated by long reads.

nltsa

R package to accompany Nonlinear Time Series by Douc, Moulines, and Stoffer

oneliners

Useful bash one-liners for bioinformatics.

orthofinder

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

orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/