We have an upcoming meeting with Illumina to discuss how the geoduck genome project is coming along and to decide how we want to proceed.

So, we wanted to get a quick idea of how well our geoduck assemblies are by performing some quick alignments using Bowtie2.

Used the following assemblies as references:

  • sn_ph_01 : SuperNova assembly of 10x Genomics data

  • sparse_03 : SparseAssembler assembly of BGI and Illumina project data
  • pga_02 : Hi-C assembly of Phase Genomics data

The analysis is documented in a Jupyter Notebook.

Jupyter Notebook (GitHub):

NOTE: Due to large amount of stdout from first genome index command, the notebook does not render well on GitHub. I recommend downloading and opening notebook on a locally install version of Jupyter.

Here’s a brief overview of the process:

  1. Generate Bowtie2 indexes for each of the genome assemblies.
  2. Map 1,000,000 reads from the following Illumina NovaSeq FastQ files:


Bowtie2 Genome Indexes:

Bowtie2 sn_ph_01 alignment folder:

Bowtie2 sparse_03 alignment folder:

Bowtie2 pga_02 alignment folder:


All mapping data was pulled from the respective *.err file in the Bowtie2 alignment folders.

sequence_ID Assembler Alignment Rate (%)
sn_ph_01 SuperNova (10x) 79.89
sparse_03 SparseAssembler 85.83
pga_02 Hi-C (Phase Genomics) 79.90|

Mapping efficiency is similar for all assemblies. After speaking with Steven, we’ve decided we’ll begin exploring genome annotation pipelines.

from Sam’s Notebook https://ift.tt/2IbDHSL

Read Mapping – Mapping Illumina Data to Geoduck Genome Assemblies with Bowtie2
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