Average Read length

Question

[serene.s]

Hello Everyone! Is there a standard tool commonly used to calculate the average read length of fastq files? If yes please mention it here because I want to know the size of average reads of my fastq files so that I can decide the cutoff for trimming the reads.

Thanks in Advance Saraswati

Answer 1

[sebastian.gregoricchio]

The most common tool that everybody uses is FastQC (link). You can download it directly as well via Conda. It gives youy many information such as per base quality (for eventual trimming of the extremities), adapter content, total amount of reads, reads length distribution, %GC etc

If you have many samples you can also generate a unique report summarizing all your data. To do that you need to analyses your fastq by fastQC (also fastq.gz it is fine, you do not need to unzip). You just put all your fastq in a folder and you run fastqc <folder path>. Then you can use multiQC (link) to generate the report of all your samples. You just need to run multiqc <path_to_folder_of_your_fastQC_results>. MultiQC could be installed via python: on the terminal, pip install multiqc.

Answer 2

[Pierre Lindenbaum]

 samtools stats in.bam  | grep "average length"

Answer 3

[colindaven]

bbmap has two great tools (via conda installable) which show read/contig distributions

readlength.sh
stats.sh