MOTIVATION: bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of analysis using a very small amount of code. bio-samtools can also be easily developed to include additional SAMtools methods and hence stay current with the latest SAMtools releases. RESULTS: We have added new Ruby classes for the MPileup and Variant Call Format (VCF) data formats emitted by SAMtools and introduced more analysis methods for variant analysis, including alternative allele calculation and allele frequency calling for SNPs. Our new implementation of bio-samtools also ensures that all the functionality of the SAMtools library is now supported and that bio-samtools can be easily extended to include future changes in SAMtools. bio-samtools 2 also provides methods that allow the user to directly produce visualization of alignment data.
MOTIVATION:bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of analysis using a very small amount of code. bio-samtools can also be easily developed to include additional SAMtools methods and hence stay current with the latest SAMtools releases. RESULTS: We have added new Ruby classes for the MPileup and Variant Call Format (VCF) data formats emitted by SAMtools and introduced more analysis methods for variant analysis, including alternative allele calculation and allele frequency calling for SNPs. Our new implementation of bio-samtools also ensures that all the functionality of the SAMtools library is now supported and that bio-samtools can be easily extended to include future changes in SAMtools. bio-samtools 2 also provides methods that allow the user to directly produce visualization of alignment data.
Authors: Elizabeth S A Sollars; Andrea L Harper; Laura J Kelly; Christine M Sambles; Ricardo H Ramirez-Gonzalez; David Swarbreck; Gemy Kaithakottil; Endymion D Cooper; Cristobal Uauy; Lenka Havlickova; Gemma Worswick; David J Studholme; Jasmin Zohren; Deborah L Salmon; Bernardo J Clavijo; Yi Li; Zhesi He; Alison Fellgett; Lea Vig McKinney; Lene Rostgaard Nielsen; Gerry C Douglas; Erik Dahl Kjær; J Allan Downie; David Boshier; Steve Lee; Jo Clark; Murray Grant; Ian Bancroft; Mario Caccamo; Richard J A Buggs Journal: Nature Date: 2016-12-26 Impact factor: 49.962
Authors: Jolanta Bondaruk; Roman Jaksik; Ziqiao Wang; David Cogdell; Sangkyou Lee; Yujie Chen; Khanh Ngoc Dinh; Tadeusz Majewski; Li Zhang; Shaolong Cao; Feng Tian; Hui Yao; Paweł Kuś; Huiqin Chen; John N Weinstein; Neema Navai; Colin Dinney; Jianjun Gao; Dan Theodorescu; Christopher Logothetis; Charles C Guo; Wenyi Wang; David McConkey; Peng Wei; Marek Kimmel; Bogdan Czerniak Journal: iScience Date: 2022-06-07