Running zAMP¶

Note

zAMP can use reads locally or from NCBI’s Sequence Read Archive (SRA).

Local reads¶

Command:

zamp run -i samples.tsv

Example samples.tsv :

sample	R1	R2	sample_group	run
SRR9067116	reads/SRR9067116_1.fastq.gz	reads/SRR9067116_2.fastq.gz	Genital_tract	run1
SRR9067115	reads/SRR9067115_1.fastq.gz	reads/SRR9067115_2.fastq.gz	Genital_tract	run1
SRR9067114	reads/SRR9067114_1.fastq.gz	reads/SRR9067114_2.fastq.gz	Genital_tract	run1
SRR7225909	reads/SRR7225909_1.fastq.gz	reads/SRR7225909_2.fastq.gz	human_biliary_tract	run2
SRR7225908	reads/SRR7225908_1.fastq.gz	reads/SRR7225908_2.fastq.gz	human_biliary_tract	run2
SRR7225907	reads/SRR7225907_1.fastq.gz	reads/SRR7225907_2.fastq.gz	human_biliary_tract	run2

sample: the name of the sample
R1: path to forward reads
R2: path to reverse reads
sample_group: sample grouping for visualizations
run: column for applying DADA2 error learning and denoising for each sequencing run

Note

You can add any other columns in the table provided the above mentionned columns are present

Command:

zamp run -i reads -m metadata.tsv

Example metadata.tsv :

fastq	sample	sample_group	run
SRR9067116	Vaginal-Library42	Genital_tract	run1
SRR9067115	Vaginal-Library41	Genital_tract	run1
SRR9067114	Vaginal-Library48	Genital_tract	run1
SRR7225909	NE14	human_biliary_tract	run2
SRR7225908	A3D12	human_biliary_tract	run2
SRR7225907	NN15	human_biliary_tract	run2

zAMP can fetch reads from NCBI’s SRA using fasterq-dump.

Command:

zamp run -i sra-samples.tsv

Example sra-samples.tsv :

sample	sample_label	sample_group	run	paired
SRR9067116	Vaginal-16s-V3V4-Library42	Genital_tract	run1	True
SRR9067115	Vaginal-16s-V3V4-Library41	Genital_tract	run1	True

sample_label: label to rename the SRA fastq files
paired: whether reads are paired or not (required because snakemake can’t guess the pairing from the fastq outputs easily )