LUSTR
LUSTR calls short tandem repeat (STR) variants from next-generation sequencing data to enable detection and characterization of germline, somatic, and multiallelic STR variation using customizable locus definitions for targeted and genome-wide analyses.
Key Features:
- Next-generation sequencing input: Processes short-read next-generation sequencing data for STR variant calling.
- Customizable locus definitions: Allows flexible definition of STR loci for targeted or genome-wide screening.
- Modular analysis framework: Provides customizable modules to tailor analyses to specific research needs or experimental conditions.
- Somatic and multiallelic calling: Supports calling of somatic STR variants and multiallelic STR alleles.
- Germline and somatic analysis: Enables both germline and somatic STR variant detection across diverse datasets.
- Assembly compatibility: Operates with predefined genome builds or novel assemblies.
- Validation: Demonstrated accuracy in inferring STR expansions using simulated and real datasets.
Scientific Applications:
- Pathogenic STR expansion detection: Identification of pathogenic STR expansions in individuals for studies of genetic disease.
- Neurological disorder research: Investigation of STR contributions to neurological disorders linked to repeat expansions.
- Genome-wide and targeted STR screens: Discovery and profiling of STR variation in genome-wide or targeted studies.
- Somatic variation studies: Analysis of somatic STR variation across tissues or disease contexts.
Methodology:
Analyzes next-generation sequencing reads to call STR variants using customizable locus definitions and modular components; operates on predefined genome builds or novel assemblies and was validated on simulated and real datasets.
Topics
Details
- Cost:
- Free of charge
- Tool Type:
- workflow
- Added:
- 5/19/2024
- Last Updated:
- 11/24/2024
Operations
Data Inputs & Outputs
Publications
Lu J, Toro C, Adams DR, Acosta MT, Adam M, Alvarez RL, Alvey J, Amendola L, Andrews A, Ashley EA, Bacino CA, Bademci G, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao H, Chinn I, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cope H, Corona R, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dickson P, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Earl D, Eckstein DJ, Emrick LT, Eng CM, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne W, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Maghiro A, Mahoney R, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Mulvihill J, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Swerdzewski BNP, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Seto E, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QK, Tan ALM, Tarakad A, Tekin M, Telischi F, Thorson W, Tifft CJ, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang L, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Moreno CAM, Lee W, Leung YY, Harms MB, Vardarajan B, Heinzen EL. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC Genomics. 2024;25(1). doi:10.1186/s12864-023-09935-9. PMID:38279154. PMCID:PMC10811831.