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A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing MIT License. Branches Tags. Nothing to show. Go back. Launching Xcode If nothing happens, download Xcode and try again. Latest commit. Git stats commits. Failed to load latest commit information. View code. Lathe A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing Installation First, install miniconda3 Then install snakemake.
This can be done with the following. Typical installation time: minutes. Change as of Lathe has been adapted to run on multiple samples simultaneously, instead of one sample per snakemake command.
If this option is selected, short read polishing will be turned on. Inputs Alter config. See above. Next, clone this github directory to some location where it can be stored permanently.
Remember to keep it updated with git pull. Don't change this. Lathe uses the Flye assembler by default. For Canu, please specify 'canu' for the assembler parameter in the config. For cluster Canu execution, please note: if set to True, you will need to install Canu, e. Please see the example config file. When executing on a cluster, Canu will appear to fail, as the first process does not produce an assembly and instead spawns subsequent jobs on the cluster.
Don't worry, just re-run Lathe when the assembly completes. To execute please run the following. Skip to content. A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing MIT License. Updated Oct 27, C. Star 6. Updated Feb 9, C. Updated Nov 23, C. Star 4. Star 3. Updated Sep 3, Eagle. Star 2. ESP32 electronic leadscrew for a lathe. Sponsor Star 2. Updated Mar 21, TypeScript. Star 1. Arduino Project for small lathes. Code Issues Pull requests Discussions.
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