User Guide Information

Sample name details

BacterialTyper accepts a wide range of files names.

Format for fastq files can be: name.fastq.gz, name_1.fastq.gz, name_R2.fastq.gz, name_L001_R1.fastq.gz, etc.

Here we provide some guidelines of the format.

Length limitation

There is a limitation for the sample ID (‘name’) of 10 characters. ** BacterialTyper provides an option to rename samples if necessary: module prep option –rename **

Single end files

It is possible to provide NGS single-end files although some steps of the process could be accomplished using single-end files. ** Use option –single-end in the different BacterialTyper modules **

name.fastq.gz

name.fastq

name.fq

Paired-end files

Paired-end files are full supported. The format for these files are:

name_1.fastq.gz or name_R1.fastq.gz

name_2.fastq.gz or name_R2.fastq.gz

Lane information:

In some cases, files might contain lane information (L00x and/or 00x). BacterialTyper supports these names as long as follow these examples:

name_L00x_R1.fastq.gz name_L00x_R2.fastq.gz

name_L00x_1.fastq.gz name_L00x_2.fastq.gz

name_L00x_R1_00x.fastq.gz name_L00x_R2_00x.fastq.gz

** If you need to merge fastq files from different lanes, use option –merge within module prep **

Extensions:

name_L00x_R2.fastq

name_L00x_R2.fq

name_L00x_R2.fastq.gz

name_L00x_R2.fq.gz