Stars
Pipeline for the extraction of the fungal 45S(SSU+ITS+LSU) and ITS from genomic data
Collection of scripts to generate sample registration forms and bulk-ena-webincli spreadsheet for high-throughput, semi-automated submission of trimmed reads to ENA.
The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.
Generate ENA taxonomy request form for generation of new species-level taxonomic IDs
A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from genome skims
Read Until client library for Nanopore Sequencing
Massively parallel phylogenetic placement of genetic sequences
Accelerated BLAST compatible local sequence aligner.
Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (colum…
A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
TULIP - The Uncorrected Long read Itegration Pipeline
Gather together a group to skill-share, co-work, and create community
Pilon is an automated genome assembly improvement and variant detection tool
Plotting scripts for long read sequencing data
A single molecule sequence assembler for genomes large and small.
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which…
Supplementary files for my book, "Bioinformatics Data Skills"