You'll need to install spacegraphcats and bcalm first.
You will also need the following files & data sets:
SRR606249.k31.abundtrim.fq.gz- Shakya et al., Podar, 2013; doi: 10.1111/1462-2920.12086; Illumina metagenome.SRR1976948.abundtrim.fq.gz- Hu et al., Banfield, 2016; doi: 10.1128/mBio.01669-15; sample SB1.
These are both k-mer trimmed. To generate from the raw SRA read sets, download the raw data from the SRA/ENA, and process as below to remove low-abundance k-mers, using scripts from khmer=2.1.2:
# both interleave-reads.py and trim-low-abund.py come from khmer==2.1.2.
interleave-reads.py ${i}_1.fastq.gz ${i}_2.fastq.gz |
trim-low-abund.py -C 3 -Z 18 -M 20e9 -V - -o $i.abundtrim.fq.gz
Look at the Snakefile for more information for what happens next!
(This is a
snakemake workflow;
execute snakemake to run it, after installing the software above.)