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bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

bioawk

BWK awk modified for biological data

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics-workbook

Bioinformatics Workbook repository

canu

A single molecule sequence assembler for genomes large and small.

chat-gpt-games

Prompts for playable games in ChatGPT

computationaltools_lessons

discovery

K-mer based classifier for Y-contig identification from Whole Genome Assemblies

dn-ds_using_paml

How to calculate dN/dS using PAML software

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

extra_ngs_related

This repository contains simple codes and functions often used in NGS (next Gen seq) and TGS (Third gen seq) analyses

fasta_summary

Summarize the contents of FASTA files.

fasta_validator

C code to validate a fasta file

fastq2highqualvcf

Scripts to process reads from FASTQ to VCF including filters

fun_projects

This repository contains some random fun projects

gaas

Genome Assembly and Annotation Service code

genome_assembly_assessment

genomeassemblytools

Genome Assembly Tools

jellyfish

A fast multi-threaded k-mer counter

maker-genome-annotations-tutorial

Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support

markdown-editor

Live (Github-flavored) Markdown Editor

mauve

A genome alignment and visualization system

mummer4

Mummer alignment tool

phyloligo

Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.

rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

seqtk

Toolkit for processing sequences in FASTA/Q formats

simple_script

pipeline and tools for personal use

statistical_tests

This is a repository containing different statistical tests written in simple R scripts that I often use when processing data obtained in the lab.

summarize-snps-with-gff

syntenyplotbyr

plot genome alignment synteny