Bioinformatician - Lotterhos Lab

Northeastern University; Nahant (MA); On-site; USD 68,000 - 96,000; Full time

Job summary

Northeastern University in Nahant, MA is seeking a Bioinformatician to build and maintain scalable pipelines for population genomics, focusing on short-read alignment and downstream analyses. You will work within the Lotterhos Lab at the Center for Marine Ecological Genomics, contributing to a large consortium project on 5,000 genomes across 100 species.

The role emphasizes reproducible workflows, collaboration with wet-lab and computational teams, and development of tutorials while handling

Qualifications

• Master's degree in biology-related field.
• 2–5 years hands-on bioinformatics with genomics.
• Proficiency with short-read aligners (BWA, Bowtie2, STAR).
• Familiarity with downstream tools (SAMtools, GATK, Picard).
• Experience writing pipelines with Snakemake or Nextflow.
• Scripting in Python, R, Bash.
• Unix/Linux command-line proficiency.
• HPC/HTC environments and schedulers (SLURM, HTCondor).
• APIs for data transfer or data movement tools.

Responsibilities

• Collaborate with network and computational teams to define data standards.
• Design and maintain scalable bioinformatics pipelines for population genomics.
• Align short-read data to reference genomes and assess mapping quality.
• Perform downstream population genomic analyses and QC.
• Document pipelines clearly for internal use and publication.
• Develop educational tutorials and assist with website development.

Skills

Python

R

Bash

UNIX/Linux

SLURM/HTCondor

HPC/HTC

APIs for data transfer

Git

Education

Master's degree in Biology, Ecology and Evolution, Bioinformatics, Computational Biology, Genetics

Tools

Snakemake

Nextflow

BWA

Bowtie2

STAR

SAMtools

GATK

Picard

Docker

Singularity/Apptainer

Job description

Bioinformatician - Lotterhos Lab

About the Opportunity

About the Center for Marine Ecological Genomics

The successful candidate will be based at the Lotterhos Lab and theCenter for Marine Ecological Genomics at Northeastern MarineScience Center in Nahant, Massachusetts. This is an in-personposition.

Job Summary

We are seeking a skilled Bioinformatician to join our consortium inMarine Macrogenomics, which seeks to create a database ofinteroperable population genomic data for 5,000 genomes from 100species. The successful candidate will play a central role indeveloping and maintaining scalable computational pipelines for theanalysis of large-scale genomic datasets, with a focus onshort-read alignment and population-level inference. This is anexciting opportunity to contribute to cutting-edge research inecological and conservation genomics.

Minimum Qualifications

Required

• Master's degree in Biology, Ecology and Evolution,Bioinformatics, Computational Biology, Genetics, or a relatedfield
• 2-5 years of hands-on experience in bioinformatics, withdemonstrated 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 systemssuch as Snakemake or Nextflow
• Solid scripting skills in Python, R, and Bash
• Comfort working on the command line, including in a Unix/Linuxenvironment
• Familiarity with high-performance computing (HPC) andhigh-throughput computing (HTC) environments and job schedulerssuch as SLURM and HTCondor
• Experience using application programming interfaces (APIs) tosend and receive data and/or experience using tools to transferlarge amounts of data between remote servers

Preferred

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

Key Responsibilities & Accountabilities

• Collaborate and coordinate with members of the network,including wet lab and computational team members, to define datastandards, ensure analytical reproducibility, and assist withproject goals
• Design, build, and maintain reproducible bioinformaticspipelines capable of scaling across many population genomicdatasets
• Align short-read sequencing data, including whole-genome andRestriction Site Associated DNA Sequencing (RADseq) datasets, toreference genomes using standard and emerging tools, and evaluatemapping quality across diverse datasets
• Perform downstream population genomic analyses, includingvariant calling, filtering, and quality control
• Document pipelines and analyses clearly for internal use andpublication
• Develop educational tutorials and assist with websitedevelopment
• Collate publicly available data and metadata, correspondingwith authors as necessary to ensure data standards

Position Type

Research

Additional Information

Northeastern has a comprehensive benefits package for benefiteligible employees. This includes medical, vision, dental, paidtime off, tuition assistance, wellness & life, retirement- aswell as commuting & transportation. Visit https://hr.northeastern.edu/benefits/ for more information.

All qualified applicants are encouraged to apply and will receiveconsideration for employment without regard to race, religion,color, national origin, age, sex, sexual orientation, disabilitystatus, or any other characteristic protected by applicablelaw.

Compensation Grade/Pay Type:

109S

Expected Hiring Range:

$67,855.00 - $95,845.00