For downstream steps you will need a genome file, genome file is a tab delimited file with chromosome names and their respective sizes. If you don’t already have a genome file follow these steps:

  1. Generate an index file for your reference, a reference file with only the main chromosomes should be used (e.g. without alternative or unplaced chromosomes).


samtools faidx <ref.fasta>


samtools faidx hg38.fasta

Faidx will index the ref file and create <ref.fasta>.fai on the reference directory.

  1. Use the index file to generate the genome file by printing the first two columns into a new file.


cut -f1,2 <ref.fasta.fai> > <ref.genome>


cut -f1,2 hg38.fasta.fai > hg38.genome

In line with the 4DN project guidelines and from our own experience optimal alignment results are obtained with Burrows-Wheeler Aligner (bwa). Prior to alignment, generate a bwa index file for the chosen reference.

bwa index <ref.fasta>


bwa index hg38.fasta

No need to specify an output path, the bwa index files are automatically generated at the reference directory. Please note that this step is time consuming, however you need to run it only once for a reference.

To avoid memory issues, some of the steps require writing temporary files into a temp folder, please generate a temp folder and remember its full path. Temp files may take up to x3 of the space that the fastq.gz files are taking, that is, if the total volume of the fastq files is 5Gb, make sure that the temp folder can store at least 15Gb.


mkdir <full_path/to/tmpdir>


mkdir /home/ubuntu/ebs/temp

In this example the folder temp will be generated on a mounted volume called ebs on a user account ubuntu.