STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci.
STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci.
复制标题
DOI：
10.1186/s13059-022-02826-4
复制
发表时间：
2022-12-14
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
短串联重复序列（STR）的扩增导致许多罕见疾病。扩增检测对于短读段DNA测序数据是具有挑战性的，因为支持读段通常被错误地映射。对于“新的”STR来说，检测特别困难，这些STR包括已知基因座上的新基序或参考基因组中不存在的STR。我们开发了STRling来有效地计数k聚体，以恢复已知和新的STR基因座处的信息性读段和调用扩增。STRling对已知的STR疾病基因座敏感，具有低错误发现率，并将新的STR扩增解析为碱基对位置准确性。它是快速的，可扩展的，开源的，可在github.com/quinlan-lab/STRling上获得。在线版本包含补充材料，可通过10.1186/s13059-022-02826-4获得。
Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for “novel” STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling. The online version contains supplementary material available at 10.1186/s13059-022-02826-4.
登录
查看更多内容
影响因子：
14.9
作者：
Highnam G;Franck C;Martin A;Stephens C;Puthige A;Mittelman D
通讯作者：
Mittelman D
影响因子：
64.8
作者：
Harris CR;Millman KJ;van der Walt SJ;Gommers R;Virtanen P;Cournapeau D;Wieser E;Taylor J;Berg S;Smith NJ;Kern R;Picus M;Hoyer S;van Kerkwijk MH;Brett M;Haldane A;Del Río JF;Wiebe M;Peterson P;Gérard-Marchant P;Sheppard K;Reddy T;Weckesser W;Abbasi H;Gohlke C;Oliphant TE
通讯作者：
Oliphant TE
影响因子：
7
作者：
Bakhtiari, Mehrdad;Shleizer-Burko, Sharona;Bafna, Vineet
通讯作者：
Bafna, Vineet
影响因子：
12.3
作者：
Dolzhenko, Egor;Bennett, Mark F.;Eberle, Michael A.
通讯作者：
Eberle, Michael A.
影响因子：
11.1
作者：
Hannan AJ
通讯作者：
Hannan AJ