Bioinformatician - Lotterhos Lab

Northeastern University•Nahant, MA

10d•Onsite

About The Position

We are seeking a skilled Bioinformatician to join our consortium in Marine Macrogenomics, which seeks to create a database of interoperable population genomic data for 5,000 genomes from 100 species. The successful candidate will play a central role in developing and maintaining scalable computational pipelines for the analysis of large-scale genomic datasets, with a focus on short-read alignment and population-level inference. This is an exciting opportunity to contribute to cutting-edge research in ecological and conservation genomics. The successful candidate will be based at the Lotterhos Lab and the Center for Marine Ecological Genomics at Northeastern Marine Science Center in Nahant, Massachusetts. This is an in-person position.

Requirements

Master's degree in Biology, Ecology and Evolution, Bioinformatics, Computational Biology, Genetics, or a related field
2-5 years of hands-on experience in bioinformatics, with demonstrated work in genomics
Proficiency in short-read alignment tools such as BWA, Bowtie2, and STAR
Familiarity with downstream processing tools such as SAMtools, Genome Analysis Toolkit (GATK), and Picard
Experience writing pipelines using workflow management systems such as Snakemake or Nextflow
Solid scripting skills in Python, R, and Bash
Comfort working on the command line, including in a Unix/Linux environment
Familiarity with high-performance computing (HPC) and high-throughput computing (HTC) environments and job schedulers such as SLURM and HTCondor
Experience using application programming interfaces (APIs) to send and receive data and/or experience using tools to transfer large amounts of data between remote servers

Nice To Haves

PhD or 3 years of post-Master's experience preferred
Experience with population genomic analyses and tools such as ANGSD, PLINK, ADMIXTURE, TreeMix, or similar platforms
Familiarity with handling non-model organism genomes or low-coverage sequencing data
Experience with version control systems such as Git and containerization technologies including Docker and Singularity/Apptainer
Track record of contributing to published research

Responsibilities

Collaborate and coordinate with members of the network, including wet lab and computational team members, to define data standards, ensure analytical reproducibility, and assist with project goals
Design, build, and maintain reproducible bioinformatics pipelines capable of scaling across many population genomic datasets
Align short-read sequencing data, including whole-genome and Restriction Site Associated DNA Sequencing (RADseq) datasets, to reference genomes using standard and emerging tools, and evaluate mapping quality across diverse datasets
Perform downstream population genomic analyses, including variant calling, filtering, and quality control
Document pipelines and analyses clearly for internal use and publication
Develop educational tutorials and assist with website development
Collate publicly available data and metadata, corresponding with authors as necessary to ensure data standards