shortle

A Pretty Ok Short-Read Assembly Workflow

How to use me

1. You'll need some reads

• Preferably paired-end
• Preferably one file each for foward and reverse reads

2. You'll need conda/mamba (recommended: mamba) and to install the main conda environment, provided by shortle.yaml in the main directory of this repository. The remaining software is provided in workflow/envs/redundans.yaml, which will be used by Snakemake, so you don't need to worry about it.

conda env create -f shortle.yaml

This command will create an environment called shortle. Activate it with:

conda activate shortle

3. You'll need to modify the first few lines that specify the forward/reverse read information in Snakefile to match your data. You'll also want to modify any parameters for sparseassembler, dbg2olc and abyss as you see fit. The values there are from previous projects and reflect those data. Adjust your k paramters accordingly (or wing it).

4. You'll need to run it once with the specific command to end it prematurely (at the purge_haplotigs stage):

snakemake -j 20 --use-conda purge_haplotigs/mapped2.bam.gencov

where j is how many cores you are willing to reserve for the Snakemake workflow.

5. Inspect purge_haplotigs/mapped2.bam.histogram.png to figure out your cutoffs as described here:

6. Modify rule purge_haplotigs_suspects to match your chosen cutoffs and rerun the entire workflow:

snakemake -j 20 --use-conda

7. Your resulting assembly will be in polish_2