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In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated\n n<\/jats:italic>\n -polymer sequences such as homopolymers (\n \n \n $$n=1$$<\/jats:tex-math>\n \n \n n<\/mml:mi>\n =<\/mml:mo>\n 1<\/mml:mn>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ) and tandem repeats (\n \n \n $$2 \\le n \\le 6$$<\/jats:tex-math>\n \n \n 2<\/mml:mn>\n \u2264<\/mml:mo>\n n<\/mml:mi>\n \u2264<\/mml:mo>\n 6<\/mml:mn>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ). At the same precision, haplotype phasing improves INDEL recall from 63.76 to\n \n \n $$70.66\\%$$<\/jats:tex-math>\n \n \n 70.66<\/mml:mn>\n %<\/mml:mo>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n and nPoRe\u00a0realignment improves it further to\n \n \n $$73.04\\%$$<\/jats:tex-math>\n \n \n 73.04<\/mml:mn>\n %<\/mml:mo>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n .\n <\/jats:p>","DOI":"10.1186\/s12859-023-05193-4","type":"journal-article","created":{"date-parts":[[2023,3,26]],"date-time":"2023-03-26T16:46:01Z","timestamp":1679849161000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["nPoRe: n-polymer realigner for improved pileup-based variant calling"],"prefix":"10.1186","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3429-4329","authenticated-orcid":false,"given":"Tim","family":"Dunn","sequence":"first","affiliation":[]},{"given":"David","family":"Blaauw","sequence":"additional","affiliation":[]},{"given":"Reetuparna","family":"Das","sequence":"additional","affiliation":[]},{"given":"Satish","family":"Narayanasamy","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,3,16]]},"reference":[{"issue":"12","key":"5193_CR1","doi-asserted-by":"publisher","first-page":"Giaa123","DOI":"10.1093\/gigascience\/giaa123","volume":"9","author":"D Lang","year":"2020","unstructured":"Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G, et al. 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