Test files to test pipeline

Question

[Deepak Tanwar]

Hello everyone,

I would like to create some small test fastq files and small reference genomes to test my pipeline.

What I have?

Few bam files.

What I want?

1. Short fastq files from my bam files.

2. Short reference genome to align those fastq files.

[Maria Kyriakidou]

For the conversion of BAM to FASTQ, you can use Bamtools: bedtools bamtofastq [OPTIONS] -i <bam> -fq <fastq> (you can check the documentation http://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html).

To make a reference genome you can get the consensus sequence of your reads using Samtools. It is going to be something like this: samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq (based on http://www.htslib.org/doc/samtools.html).

If you need a smaller genome in general to align your reads against to it, you can get a subsequent of the genome of your interest.

[GenoMax]

samtools fastq will do the fastq conversion, if you want to stay all within samtools.

[GenoMax]

Between reformat.sh (to get the fastq) and tadpole.sh (to assemble those into a reference) BBMap Suite may have you covered.