RagTag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging RagTag also provides command line utilities for working with common genome assembly file formats. Location and version: 1 2 3 4 $ which ragtag.py /local/cluster/bin/ragtag.py $ ragtag.py --version v2.1.0 help message: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 $ ragtag.

PEAR - Paired-End reAd mergeR PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

MaSuRCA Genome Assembly and Analysis Toolkit Quick Start Guide The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner. The usage instructions for the additional tools that are exclusive to MaSuRCA, such as POLCA and Chromosome scaffolder are provided at the end of this Guide.

antiSMASH antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. To activate: 1 2 bash source /local/cluster/antismash/activate.sh To use in SGE: Make a bash script and put the source /local/cluster/antismash/activate.sh before your antismash commands, and submit the script using SGE_Batch or SGE_Array.

gtt gtt is a fully featured command line interface for GitLab’s time tracking feature. It monitors the time you spent on an issue or merge request locally and syncs it to GitLab. It also allows you to create reports in various formats from time tracking data stored on GitLab. Location and version: 1 2 3 4 $ which gtt /local/cluster/bin/gtt $ gtt --version 1.7.40 help message: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 $ gtt --help Usage: gtt [options] [command] Options: -V, --version output the version number -h, --help output usage information Commands: start [project] [id] start monitoring time for the given project and resource id create [project] [title] start monitoring time for the given project and create a new issue or merge request with the given title status shows if time monitoring is running stop stop monitoring time resume [project] resume monitoring time for last stopped record cancel cancel and discard active monitoring time log log recorded time records sync sync local time records to GitLab edit [id] edit time record by the given id delete [id] delete time record by the given id report [project] [ids] generate a report for the given project and issues config edit the configuration file in your default editor help [cmd] display help for [cmd] tutorial Create personal access token https://gitlab.

BUSCOv5 - Benchmarking sets of Universal Single-Copy Orthologs. For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html Main changes in v5: Metaeuk is used as default gene predictor for eukaryote pipeline. Augustus is maintained and can be used optionally instead of Metaeuk. Introduction of batch mode: input argument can be a folder containing input files The folder structure has changed, so if doing a manual installation, make sure to completely remove any previous versions of BUSCO before installing v5.