Raven Raven is a de novo genome assembler for long uncorrected reads. Using in SGE_Batch Make sure you are in bash, and generate a shell script with your commands that you want to submit over SGE. Add the source /local/cluster/raven/activate.sh line before your commands to access the programs over SGE. To activate: 1 2 bash source /local/cluster/raven/activate.sh Location and version: 1 2 3 4 $ which raven /local/cluster/raven/bin/raven $ raven --version 1.

Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. For installation instructions, usage, deeper explanations and more, head over to the Polypolish wiki! Location and version:

Trycycler Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs. For installation instructions, usage, deeper explanations and more, head over to the Trycycler wiki! Using in SGE_Batch Make sure you are in bash, and generate a shell script with your commands that you want to submit over SGE.

LINKS Long Interval Nucleotide K-mer Scaffolder LINKS v2.0.0 René L. Warren, Yaman Malkoc, T. Murathan Goktas 2014-2022 email: rwarren [at] bcgsc [dot] ca Description LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.

MMseqs2: ultra fast and sensitive sequence search and clustering suite MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST.

GetOrganelle This toolkit assemblies organelle genome from genomic skimming data. It achieved the best performance overall both on simulated and real data and was recommended as the default for chloroplast genome assembly in a third-party comparison paper (Freudenthal et al. 2020. Genome Biology). Conda env activation You must activate the conda env to use this software. To activate: 1 2 bash source /local/cluster/getorganelle/activate.sh Location and version: 1 2 3 4 5 6 $ which get_organelle_from_reads.