SeqMap 3

Introduction

It is important to determine where integrations take place when foreign DNA is introduced into target genomes. Profiling viral integration sites is much more critical in evaluating the safety of gene therapy viral vector. In recent years, LAM-PCR and nrLAM-PCR coupled with next-generation sequencing has become a standard approach to characterize viral integration sites in gene therapy. A few bioinformatics tools are available to analyze the sequencing data derived from high-throughput multiplexed sequencing of LAM-CPR/nrLAM-PCR amplicons. Here we implement a new bioinformatics pipeline, SeqMap3. Unlike the several published tools that use BLAST or BLAT to identify VIS, we instead utilize the well developed and widely used short reads alignment tools bowtie in SeqMap 3. It is orders of magnitude faster than BLAST and BLAT.

Access to SeqMap 3

To access SeqMap3 you must have an NGVB account. If you do not currently have one click here to register for NGVB account. Once you have an account read quick guide to using the system below or click here to login to SeqMap (Use your email and password from NGVB account).

Quick Guide to SeqMap 3

Once you have all of your files uploaded you can run your data through the SeqMap3 pipeline. ( click here for the full guide to learn how to upload)
  1. Under the Tools menu click on the Seqmap Pipeline - Paired End link (or Single End link if you wish to run a Single End job - steps to run the job is the same for both)
  2. In the first field Read 1 there is a dropdown of all of your uploaded fastq files. Only fastq files will show up in this drop down. Select your Read 1 fastq file.
  3. Select your Read 2 file. This is the same type of dropdown as the first where only fastq files will be available to select.
  4. Choose whether the reference genome is Mouse (mm10) or Human (hg19). If you wish to run your job against a different genome please contact us.
  5. Enter by typing or pasting your LTR Primer
  6. Enter by typing or pasting your Linker Primer
  7. Select your Viral Vector from the dropdown. This dropdown is similar to the first 2, but it list only fasta files.
  8. Select your Internal Control from the dropdown.
  9. Give this Job a name you wish to identify it by.
  10. Click the Execute button to run the job.