Search results

...ble improvement of SOAPaligner is that it now supports a wide range of the read length.

...tive splicing events from the graph and quantifies the events based on the alignment data. The quantified events can then be used for differential analysis.

...ses within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the comman ...J., Lindgreen, S., & Krogh, A. (2014). Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC bioinformatics, 15(1),

[[Category:Software]][[Category:Biology]][[Category:Alignment]] This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pur

...mple quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation u ...nt statistics, feature counting and feature annotation for long- and short-read sequencing. Bioinformatics. 2019 Jul 15;35(14):2489-2491. https://doi.org/1

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

...based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe, while diverged plasmids can be predicted using order-s

...ates on BAM alignment files, which are produced by most contemporary short-read aligners.

...stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:

...with high sensitivity (≥94%) for various read lengths. In particular, for short Illumina reads (~45-75 bp) it makes about 4% more assignments as compared t By implementing Blat a faster alignment method as opposed to Blastx (though both options are available), the analys