DemuxFastqs with multiple FASTQs per Read

August 17, 2019Bioinformatics No Comments

The DemuxFastqs tool in fgbio is a flexible tool for sample demultiplexing. It takes FASTQs as input, one per sub-read (ex. index read, read one, read two, fragment). You tell it which bases are part of the sample barcode, molecular barcode, and template, and which should be ignored (see Read Structures). Some sequencers (ex. MiSeq) … Read More

Sequencing Error-reduction through Consensus Calling Reads from the same Source Molecule

August 4, 2017Bioinformatics No Comments

Dramatic sequencing error-reduction can be achieved through calling consensus reads that observe the same source molecule.   This is extremely important for low-frequency variant detection in somatic samples, as well as genotyping STRs (short-tandem repeats) where high rates of “stutter” can be overcome.  I will review the method behind calling consensus reads. There are two … Read More

Single Strand UMI Somatic Variant Calling

July 5, 2017Bioinformatics No Comments

Somatic tumor-only variant calling can be improved by incorporating a UMI per-strand on the source molecule.  You can also perform Duplex Sequencing (see Kennedy et al 2014) but I will go into that in a later post.   Below I will detail the process as well as give you a command line tool that automates all … Read More

Sample Demultiplexing an Illumina Sequencing Run

June 25, 2017Bioinformatics No Comments

Sample demultiplexing an Illumina sequencing run can be a real pain if you’re the one having to do it. Typically you would just let the instrument do it for you, or perhaps even use Illumina’s bcl2fastq, but sometimes you don’t have that choice.  You may only have access to the run folder, loathe making FASTQ … Read More