List of fastq files containing the first mate of raw reads. Muliple files are provided if multiplexing of the same library has been done on multiple lanes. The reads comming from different fastq files are pooled after alignment. Also see parameter \"fastq2\".

List of fastq files containing the second mate of raw reads in case of paired end (also see parameter \"fastq1\"). Important: this list has to be of same length as parameter \"fastq1\" no matter if paired or single end is used. In case of single end data specify \"null\" for every entry of fastq1.

Path to reference genome in fasta format. Bowtie2 index files (\".1.bt2\", \".2.bt2\", ...) as well as a samtools index (\".fai\") has to be located in the same directory.\n All of these files can be downloaded for the most common genome builds at https://support.illumina.com/sequencing/sequencing_software/igenome.html. Alternatively, you can use \"bowtie2-build\" or \"samtools index\" to create them yourself.

Adapter sequence for first reads. If not specified (set to \"null\"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to \"illumina\", \"nextera\", or \"small_rna\". Or you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").

Adapter sequence for second reads (only relevant for paired end data). If it is not specified (set to \"null\"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to \"illumina\", \"nextera\", or \"small_rna\". Or you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").

Bin size used for generation of coverage tracks. The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1.

Sample ID used for naming the output files.

Mean library fragment size, used to reconstruct entire fragments from single end reads. Not relevant in case of paired end data.

If paired end data is used set to true, else set to false.

Path to reference genome of the spike-in organism in fasta format. Bowtie2 index files (\".1.bt2\", \".2.bt2\", ...) as well as a samtools index (\".fai\") has to be located in the same directory.\n All of these files can be downloaded for the most common genome builds at https://support.illumina.com/sequencing/sequencing_software/igenome.html. Alternatively, you can use \"bowtie2-build\" or \"samtools index\" to create them yourself.

The effectively mappable genome size, please see: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html

List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. Specify as space-delimited string. Default: \"chrX chrY chrM\"