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