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bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean
2012 Open Research Computation  
developed bio-samtools, a Ruby binding to the SAMtools library.  ...  The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses.  ...  Most high-throughput alignment programs produce a standard output file in Sequence Alignment/Map format (SAM) [6] , a tab-delimited text-based format for describing alignments.  ... 
doi:10.1186/2042-5767-1-1 fatcat:wm27nslkyfcflhorouywd6r7hm

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean
2012 Source Code for Biology and Medicine  
developed bio-samtools, a Ruby binding to the SAMtools library.  ...  The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses.  ...  Most high-throughput alignment programs produce a standard output file in Sequence Alignment/Map format (SAM) [6] , a tab-delimited text-based format for describing alignments.  ... 
doi:10.1186/1751-0473-7-6 pmid:22640879 pmcid:PMC3473260 fatcat:uzpwqxejurgyxdprzm2hc6vn64

Mapping mutations in plant genomes with the user-friendly web application CandiSNP

Graham J Etherington, Jacqueline Monaghan, Cyril Zipfel, Dan MacLean
2014 Plant Methods  
Mapping mutations by position, either using classical methods or whole genome high-throughput sequencing (HTS), largely relies on the analysis of genome-wide polymorphisms in F 2 recombinant populations  ...  It is particularly useful for analysing HTS data from bulked back-crossed mutants, which contain fewer polymorphisms than data generated from out-crosses.  ...  Frederikke Gro Malinovsky for careful reading of the manuscript and all members of the MacLean and Zipfel laboratories for helpful suggestions. Martin Page is acknowledged for technical assistance.  ... 
doi:10.1186/s13007-014-0041-7 pmid:25610492 pmcid:PMC4301057 fatcat:agqe2dplmfad5oreshzgtksuom

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans [article]

David Sebastian Jimenez, Jun Kim, Bhavana Ragipani, Bo Zhang, Lena Annika Street, Maxwell Kramer, Sarah Elizabeth Albritton, Lara Winterkorn, Sevinc Ercan
2021 bioRxiv   pre-print
On the X chromosome, strong rex sites contain multiple copies of a 12-bp sequence motif and act as TAD borders.  ...  Condensins are molecular motors that compact DNA for chromosome segregation and gene regulation.  ...  ., Bio-samtools: Ruby bindings for SAMtools, a library for 21 accessing BAM files containing high-throughput sequence alignments. Source Code Biol 22 Med, 2012. 7(1): p. 6. 23 53.  ... 
doi:10.1101/2021.03.23.436694 fatcat:z3bq7keuuvfipoq5yuhelbdukq