Ben J Woodcroft

CoverM. Read alignment statistics for metagenomics

kingfisher-download. Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

singlem. Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

galah. More scalable dereplication for metagenome assembled genomes

OrfM. simple and not slow ORF caller

goruby. Gene Ontology (GO) interface for Ruby

rarff. (fork) A Ruby library for handling ARFF files, as popularized by the WEKA machine learning program

sandpiper. Website / continuous DB builds for SingleM

bbbin. A collection of working and non-working bioinformatics scripts

bacterial_dating_aerobic_predictor. Prediction of aerobicity in extant and ancient genomes

smafa. Biological sequence aligner for pre-aligned sequences

bioruby-sra. Ruby interface to the NCBI Sequence Read Archive (SRA)

hmmer-rs. Ergonomic Rust interface to HMMER

singlem-benchmarking. Jupyter Notebook

bioruby-cigar. A parser for CIGAR format alignments

bioruby-kmer_counter. A biogem for counting small kmers for fingerprinting nucleotide sequences

finishm. genome improvement and finishing without further sequencing effort

dirseq. Work out whether RNAseq reads in general agree with the direction of the gene predicted

scim. (Unofficial) Smart Common Input Method

bioruby-ipcress. Parser for the ipcress in-silico PCR program

bioruby-signalp. A wrapper for the signal peptide prediction algorithm SignalP

bioruby-orthomcl. Ruby wrappings and useful methods for the OrthoMCL database of protein orthology

mfqe. FASTA/FASTQ extractor for multiple sets of read names

bioruby-tm_hmm. A bioruby plugin for interaction with the transmembrane predictor TMHMM

guix. Scheme

bioruby-gag. bio-gag is a biogem for detecting and correcting a particular type of error (gag errors) that occurs/occurred in a particular version of the IonTorrent sequencing kit.

reach. Extend the Ruby Array class for less loops and blocks

blast_link. A few scripts for turning a vanilla NCBI wwwblast installation into a link filled paradise.

bird_tool_utils-rust. Utility functions for the bird metagenomic toolkit

bioruby-hmmer3_report. Parser for hmmsearch and hmmscan in the HMMER 3 package.

reubypathdb. Ruby classes for parsing EuPathDB database download files from PlasmoDB, ToxoDB, CryptoDB, TriTrypDB, PiroplasmaDB and FungiDB, etc.

ace2sam. (fork) Converts an ACE alignment to a SAM file

bioruby-cnls_screenscraper. a bioruby plugin for interaction with the cNLS (classical Nuclear Localisation Signal) predictor

tree2tax2. Assign branch-length based taxonomy to trees free from the 7 levels

bioruby-img_database. An activerecord-based offline database mirroring the Integrated Microbial Genomes (IMG) resource

bioruby-newbler_outputs. Parsers for outputs from the assembly program Newbler

bioruby-wolf_psort_wrapper. Enables the localisation predictor WoLF PSORT to be run locally

bioruby-krona. Programmatic interface to krona visualisations

singlem-installation. Containerised testing of SingleM installation methods

biouby-agp. A Ruby parser of AGP format assembly scaffolding files

amplicon_encyclopaedia. TODO: one-line summary of your gem

bioruby-exportpred. Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins

bird_tool_utils-python. Opinionated Python utilities used in the bird suite of bioinformatic tools, developed by the Woodcroft lab

bioruby-cog_categories. API to Clusters of Orthologous Groups of proteins (COGs) functional categories

bioruby-aliphatic_index. TODO: one-line summary of your gem

singlem_extra_packages. Extra SingleM packages not included in the base distribution

prodigal-runner. Run prodigal on microbial genomes automatically choosing between translation tables 4 and 11.

tree2tax. Automatic taxonomy through consistent application of tree-based thresholding

yargraph. Another Ruby graph (in the nodes and edges sense of the word) library

bioruby-hmmer_model. Parse PFAM HMM definition files