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agouti

Annotated Genome Optimization Using Transcriptome Information

augustus

Genome annotation with AUGUSTUS

biocode

Bioinformatics code libraries and scripts

comparative-annotation-toolkit

comparem

A toolbox for comparative genomics.

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species.

flye

De novo assembler for single molecule sequencing reads using repeat graphs

football-analytics

Visualizations and predictive analytics which uses statsbomb and other data sources to visualize metrics like shot location, through ball pass, passmap, heatmap of a player, xG of a shoot etc.

fusariumlifestyles

Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085

gff3toolkit

Python programs for processing GFF3 files

mashmap

A fast approximate aligner for long DNA sequences

pipelines-nextflow

NBIS nextflow pipelines framework

pycoqc

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

qtl-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype

quast

Genome assembly evaluation tool

shasta

De novo assembly from Oxford Nanopore reads.

slr-superscaffolder

A scaffold assemble pipeline for stLFR reads.

threshold-for-bulk-segregant-analysis

This script is written by my lab member, Jenny. I used this script to determine the cut-off of allele frequency for bulk segregant analysis.

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

vlte_pipelines

Pipelines for fitness assay, sequencing, etc. analysis of the VLTE ("very" long term evolution experiment (yeast))