Bioinformatician - Lotterhos Lab

Northeastern University; Northern (KY); Hybrid; USD 68,000 - 96,000; Full time

Job summary

Northeastern University’s Lotterhos Lab in Nahant, MA seeks a Bioinformatician to design and maintain scalable pipelines for large-scale genomic data, with emphasis on short-read alignment and population inference.

The role is in-person and requires a Master’s in a related field, 2–5 years of experience, and hands-on expertise with BWA, Bowtie2, STAR, GATK, SAMtools, Snakemake/Nextflow, and HPC environments. You will collaborate across wet lab and computational teams.

Qualifications

• Master's degree in biology or related fields.
• 2–5 years of hands-on bioinformatics experience in genomics.
• Proficiency with short-read alignment tools (BWA, Bowtie2, STAR).
• Familiarity with SAMtools, GATK, Picard; experience with pipelines (Snakemake/Nextflow).
• Strong scripting in Python, R, Bash; Unix/Linux command line comfort.
• Experience in HPC/HTC environments and schedulers (SLURM/HTCondor).
• Experience using APIs for data transfer and remote servers.

Responsibilities

• Design, build, and maintain scalable bioinformatics pipelines for population genomics.
• Align short-read sequencing data to reference genomes and assess mapping quality.
• Perform downstream analyses: variant calling, filtering, QC.
• Document pipelines for reproducibility and publication.
• Develop tutorials and assist with website development.
• Collaborate with wet lab and computational teams to standardize data.

Skills

Python

R

Bash

Unix/Linux

HPC/HTC experience

APIs / data transfer

Education

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

Tools

BWA

Bowtie2

STAR

SAMtools

GATK

Picard

Snakemake

Nextflow

Git

Docker

Singularity/Apptainer

SLURM

HTCondor

Job description

## Bioinformatician - Lotterhos LabApply: Nahant, MA: Full time: Posted Today: R142449**About the Opportunity** **About the Center for Marine Ecological 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. **Job Summary**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. **Minimum Qualifications****Required*** 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**Preferred*** 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 **Key Responsibilities & Accountabilities*** 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**Position Type**Research**Additional Information**Northeastern University considers factors such as candidate work experience, education and skills when extending an offer.Northeastern has a comprehensive benefits package for benefit eligible employees. This includes medical, vision, dental, paid time off, tuition assistance, wellness & life, retirement- as well as commuting & transportation. Visit https://hr.northeastern.edu/benefits/ for more information.All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, religion, color, national origin, age, sex, sexual orientation, disability status, or any other characteristic protected by applicable law.**Compensation Grade/Pay Type:**109S**Expected Hiring Range:**$67,855.00 - $95,845.00*With the pay range(s) shown above, the starting salary will depend on several factors, which may include your education, experience, location, knowledge and expertise, and skills as well as a pay comparison to similarly-situated employees already in the role. Salary ranges are reviewed regularly and are subject to change.*