cloc counts blank lines, comment lines, and physical lines of source code in many programming languages.

Enjoy the mysteries of the sea from the safety of your own terminal!

⚡ ♒ Rapid prokaryotic genome annotation

Automatically exported from code.google.com/p/cdhit

✂️ ⚡ Rapid haploid variant calling and core genome alignment

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

🔬 ♌ Bacterial ribosomal RNA predictor

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

A scalable high-throughput metabolic and biogeochemical functional trait profiler

Phylogenetic and taxonomic analysis for genomes and metagenomes

Scripts and tutorials on how to assemble individual microbial genomes from metagenomes

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

Colorize input filenames just like ls(1) does

PaperBLAST: find papers about a protein or its homologs

Metagenomic pipeline and other general scripts used in the lab.

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE …

Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Comm…

Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses t…

Snakemake pipeline for annotating metagenome-assembled genomes (MAGs) (pronounced mag-pie)

a collection of scripts I have used in bioinformatic analyses

Operational taxonomic unit (OTU) classification based on phylogenetic tree structures

Files for the SBDI Sativa curated GTDB 16S sequence files

This repository contains the artificats related to development and evaluation of the method:CoMet: A workflow using contig coverage and composition for binning a metagenomic sample with high precision