{"id":2458520,"url":"https://alion.io/job/ontrac-solutions-software-engineer-bioinformatics-pipelines","title":"Software Engineer – Bioinformatics Pipelines","company":{"id":2634,"name":"Ontrac Solutions","domain":"ontracsolutions.net","url":"https://alion.io/company/ontrac-solutions","size_band":"51-200","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Breezy","truth_index":{"grade":"B","score":75,"open_postings":8,"ghost_share":0,"stale_share":1,"repost_share":0,"time_to_fill_p50_days":null,"computed_at":"2026-10-15T05:46:00Z"}},"role":"Backend","role_family":"Backend","seniority":null,"employment_type":"contractor","work_mode":"remote","remote_scope":"stated_countries","remote_scope_basis":"posting_text","remote_working_hours":null,"hiring_geo_confidence":"explicit","locations":["Chicago, United States"],"countries":["US"],"hiring_countries":["US"],"hiring_countries_total":1,"salary":null,"salary_estimate":{"min_usd":123000,"max_usd":259000,"period":"year","method":"role_country_seniority_unknown","sample_n":8485},"experience_years_min":null,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Agile","optional":false},{"name":"HPC","optional":false},{"name":"Python","optional":false}],"status":"live","first_seen_at":"2026-09-23T21:32:29Z","employer_posted_date":"2026-09-23","last_verified_at":"2026-10-15T19:15:12Z","board_verified":true,"closed_at":null,"days_open":21,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":21},"description":"OVERVIEW\nOnTrac is seeking a highly skilled and experienced Software Engineer (Bioinformatics Pipelines) to join a contractor program supporting a critical customer engagement: the genomics unit of a healthcare customer, which requires a temporary software engineer on its pipeline teams for the next 12 to 18 months. The need is driven by a short-term increase in workload from an organization-wide transition of the Laboratory Information System (LIS) from Soft to Epic Beaker.\nThis role is ideal for a software engineer with a strong background in bioinformatics who can integrate into an established pipeline team quickly and begin contributing with limited ramp-up. It is not suited to a biologist with some programming skills; the work centers on the engineering of the pipelines (software quality, performance, automation, and operational support) rather than on scientific discovery. The successful candidate will work closely with the delivery team and customer stakeholders, including the customer's dedicated bioinformatics team, to ensure project success from initial definition through final delivery.\nENGAGEMENT\nExpected start date: 2 November 2026\nDuration: 12 to 18 months\nLocation: United States only, fully remote\nREQUIRED CREDENTIALS\nProfessional software engineering experience with a demonstrated background in bioinformatics pipeline engineering\nHands-on production experience with Python, Bash, and Nextflow\nREQUIRED QUALIFICATIONS\nStrong software engineering fundamentals applied to bioinformatics pipelines, with a focus on software quality, performance tuning, automation, and operational support\nProficiency in Python and Bash\nExperience with Nextflow for workflow management\nExperience developing, tuning, and operating pipelines in an on-premise high-performance computing (HPC) environment\nExperience integrating software with laboratory systems and sequencing instruments\nExperience working as a member of an agile team\nAbility to integrate into an established team quickly and contribute with limited ramp-up\nUSEFUL QUALIFICATIONS\nDirect experience with Illumina, Oxford Nanopore, or PacBio sequencing platforms\nSCOPE AND DELIVERY EXPECTATIONS\nThe following covers the scope of work we anticipate the contractor supporting throughout the project. This scope is in line with our expectations of the project but is subject to change.\nMaintain and improve the software quality of the genomics pipelines running in the customer's on-premise HPC environment\nTune the performance of the pipelines in the HPC environment\nAutomate pipeline operations and recurring engineering tasks\nProvide operational support for the pipelines, including troubleshooting failures and resolving issues in the movement and delivery of genomic data\nImplement and maintain integrations between the pipelines and laboratory systems and sequencing instruments, including Illumina, Oxford Nanopore, and PacBio platforms\nImplement and maintain the technical infrastructure that enables the movement, analysis, and delivery of genomic data, working alongside the customer's bioinformatics team, which owns the biological aspects of the analyses\nSupport the additional pipeline workload arising from the organization-wide LIS transition from Soft to Epic Beaker\nParticipate as a full member of an agile pipeline team for the duration of the engagement","description_format":"text","description_chars":3350,"description_truncated":false,"requirements":{"experience_years_min":null,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":null,"security_clearance":false,"languages":[]},"benefits":[],"hiring_locations":[{"name":"United States","iso":"US","kind":"country"}],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics","Predictive Analytics","AI Consulting & Integration","Cloud Consulting & Migration"],"lifecycle":[{"event":"open","at":"2026-10-13T16:41:22Z"}],"visa":[],"liveness":{"score":73,"band":"hot","label":"Hiring now","p_open":1,"p_active":0.81,"p_room":0.9,"age_days":21,"expected_fill_days":39,"reasons":["conf:1","velocity","win:mid"],"computed_at":"2026-10-15T05:46:00Z"},"pay":null,"html_url":"https://alion.io/job/ontrac-solutions-software-engineer-bioinformatics-pipelines","json_url":"https://alion.io/job/ontrac-solutions-software-engineer-bioinformatics-pipelines.json","meta":{"generated_at":"2026-10-15T21:27:38Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","about":"Alion is a live layer of people, companies and AI agents: who they are, whether they are real and active right now, what they do and how to work with them, readable by people and by agents and paid per call.","catalog":"https://alion.io/catalog.json","usage":{"tier":"crawler_verified","counted_by":"address","units_charged":1,"used_today":32585,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-10-16T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.02,"usd":0.002,"plus_per_slice":{"credits":0.05,"usd":0.005}},"unit":"per company, plus each slice with data","note":"the employer in depth","call":{"mcp_tool":"get_company","arguments":{"id":2634},"rest":"https://alion.io/mcp/rest/get_company?id=2634"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Fontrac-solutions-software-engineer-bioinformatics-pipelines"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"live","price":{"credits":1,"usd":0.1},"unit":"per slice","note":"pay, demand and time to fill for this role and place","call":{"mcp_tool":"market_stats"},"human":"https://alion.io/catalog?offer=market.stats&for=job%2Fontrac-solutions-software-engineer-bioinformatics-pipelines"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.02,"usd":0.002},"unit":"per posting in a list","note":"similar open postings","call":{"mcp_tool":"search_jobs"},"human":"https://alion.io/catalog?offer=job.search&for=job%2Fontrac-solutions-software-engineer-bioinformatics-pipelines"},{"id":"company.verify","title":"Is this company real and active right now","status":"pilot","price":null,"unit":"per company","request":{"url":"https://alion.io/catalog/request","method":"POST","body":"{\"offer\": \"company.verify\", \"for\": \"job/ontrac-solutions-software-engineer-bioinformatics-pipelines\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Fontrac-solutions-software-engineer-bioinformatics-pipelines"}]}