InputFile.md

Table format for providing read files

This pipeline is designed to run parallel on a large number of samples. Since every sample can contain several read files in fastq format the input is provided in the form of a tabular input file. It must have the followin format

Sample_Id	Long_Reads	Short_Reads_1	Short_reads_2
testSet	testReads/testReads_nanopore.fastq.gz	testReads/testReads_illumina_S1.fastq.gz	testReads/testReads_illumina_S2.fastq.gz

Content of the columns:

1. Sample_Id Unique identifier to this sample, will be to label output files.
2. Short_Reads_1 Path to .fastq.gz file with part 1 of Illumina paired end reads.
3. Short_Reads_2 Path to .fastq.gz file with part 2 of Illumina paired end reads.
4. Long_Reads Path to .fastq.gz file containing long reads

See also the includede Testfile samples_test.tsv for reference.

Multiple Nanopore ReadFiles:

• If you have several FastQ files for one sample, which is sometimes the case for ONT basecalling output you need to combine them before using them in this pipeline. (zcat file1.fastq.gz file2.fastq.gz > combined.fastq.gz)