linsalrob Goto Github PK

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

fast-adapter-trimming

Quickly remove adapters from DNA sequence files

fasta_validator

C code to validate a fasta file

fastdemux

A program to demultiplex fastq files

fastpath

A program to find the path through a network of nodes.

fastq-pair

Match up paired end fastq files quickly and efficiently.

focus

A model to identify organisms present in metagenomes in seconds

fuzzymetabolicmodeling

This is code from Rob Edwards' bioinformatics group about fuzzy metabolic networks and their implementations to solve challenges in microbial genomics and metagenomics

genbank_to

Convert genbank files to a swath of other formats

genetic_codes

Python code for translating sequences using different NCBI translation tables and genetic codes.

genotype-phenotype-modeling

Modeling growth of bacterial genomes and connecting genotype to phenotype

get_orfs

C code to translate a DNA sequence using different translation tables. Designed to be fast and lightweight, with few dependencies (only zlib and pthreads)

gretel

An algorithm for recovering haplotypes from metagenomes

gretel-test

hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

jetstream-search-sra

Search the SRA using the jetstream sra cluster setup

jetstream-search-sra-proteins

Use diamond to search the SRA

jetstream-sra-cluster-setup

This module sets up an autoscaled Jetstream cluster for SRA work, based on HTCondor, the OpenStack Shade library, and SaltStack.

linsalrob.github.io

the linsalrob github.io pages

mgi-adapters

Trim adapters from MGI sequence data

multiphate

Throughput PhATE processing of draft or finished phage genomes

multiphate2

multiPhATE with comparative genomics

pacer-hackathon-2023

PaCER Hackathon 2023 documentation and attendee guide

partie

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 allows automatic separation of the data.

partie_hat

High throughput automated typing for the partition engine

pbj_placer

Rewrite jplacer files from phylosift for importing into ITOL and other tree viewing software

phagehosts

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

phageproteomictree

The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance

phanns

phanotate

PHANOTATE: a tool to annotate phage genomes.