bactopia/bactopia: More tools, more input options, additional analyses!

Major changes in v1.4.0 of Bactopia! Some key changes: New Bactopia Tools (eggNOG-mapper, ISMapper, Mashtree, PIRATE) Pre-assembled genomes as inputs Hybrid assembly (Unicycler) Assembly assessments (QUAST, CheckM) Many, many more, full details below! Installation Conda: conda create -n bactopia -c conda-forge -c bioconda bactopia Docker: docker pull bactopia/bactopia Singularity: singularity pull library://rpetit3/bactopia/bactopia v1.4.0 bactopia/bactopia "Archer's Ring" - 2020/07/01 Added New Bactopia Tools eggnog for functional annotation using eggNOG-mapper mashtree to create a tree using Mash distances pirate to create pangenome using PIRATE ismapper for insertion site discovery Documentation for new tools and tweaks to existing BTs roary and pirate can now be run on just completed genomes Can limit number of completed genomes downloaded where applicable bactopia datasets can provide list of RefSeq accessions to download bactopia search can now use BioSample and Run accessions bactopia search can select a subset of Experiments associated with a BioSample Support for organisms with multiple MLST schemas Assembly QC via QUAST and CheckM Assemblies (local or NCBI Assembly accession) as inputs for Bactopia Long reads as supplementary to paired end reads for hybrid assembly Tools versions are locked to the minor version, not the patch Fixed summary will now determine absolute path of inputs fastani improved user reference import went back a version on call_variants openjdk version all bactopia tools now put nextflow info in the same folder as outputs Typos in docs Bactopia Tools now check existence of include and exclude files Lots more documentation Updated citations/tools used by Bactopia Did I mention typos? Removed ISMapper as part of the main pipeline (its now a tool) insertion-sequences in bactopia dataset