kreeq

The standard notation for using kreeq is as follows:

kreeq validate -f input.[fasta|fastq][.gz] -r reads1.fastq[.gz] reads2.fastq[.gz] [...] [-k 21]

It accepts multiple read files as input, separated by space. The two modes we will be using today are validate and union. To check out all options and flags use:

kreeq -h
kreeq validate -h
kreeq union -h

Let's get some test files first:

mv gfastar/docs/testFiles-kreeq/* .

We will test some typical usage with the files moved from the testFiles folder, e.g.:

kreeq validate -f random1.fasta -r random1.fastq
kreeq validate -f random2.fasta -r random1.fastq random2.fastq

Importantly, the kreeq database can only be computed once on the read set, and reused for multiple analyses to save runtime:

kreeq validate -r random1.fastq -o random1.kreeq
kreeq validate -f random1.fasta -d random_fa.kreeq

Similarly, kreeq databases can be generated separately for multiple inputs and combined, with increased performance in HPC environments:

kreeq validate -r random1.fastq -o random1.kreeq
kreeq validate -r random2.fastq -o random2.kreeq

kreeq union -d random1.kreeq random2.kreeq -o union.kreeq
kreeq validate -f random1.fasta -d union.kreeq

Now working with real sequencing data:

Let's start by running gfastats to get a sense of what we are evaluating:

gfastats input.fa

Now we are ready to run kreeq:

kreeq validate -r filtered.fastq -o filtered.kreeq
kreeq validate -r filtered2.fastq -o filtered2.kreeq

kreeq union -d filtered.kreeq filtered2.kreeq -o filtered_union.kreeq

kreeq validate -f input.fa -d filtered_union.kreeq