Join us for a webinar: The complexities of spatial multiomics unraveled
May 2
Page History
...
Alignment tools appear in the context-sensitive menu on the right of the screen (Figure 1) when click on any data node containing FASTQ files. Examples include Unaligned reads, Trimmed reads, and Subsampled reads data nodes.
...
GSNAP5 (Version 2015-12-31(v8)) - A short read aligner (>14bp) using a successive constrained search, capable of handling splicing using either a probabilistic model or database. Built to handle SNPs in alignment. Good sensitivity but slower speed and higher memory usage. Popular for RNA-seq analysis. (http://research-pub.gene.com/gmap/)
HISAT2 HISAT26 (Version 2.1.0) - A fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of genomes. HISAT2 is a successor to TopHat2. (https://github.com/DaehwanKimLab/hisat2)
Isaac 26 7 (Version 15.07.16) - Gapped aligner that finds candidate mapping positions by matching 32-mers from the data to 32-mers from the reference, extending the candidate mappings to the whole read, and selecting the best mapping. Has utility for mappying DNA-Seq with good speed and accuracy but high memory usage. (https://github.com/Illumina/isaac2)
STAR7 8 (Version 2.6.1d) - Splice-aware aligner that utilizes novel sequential maximal mappable seed search capable of handling splice junctions. Seeds are subsequently stitched together by local alignment. Capable of handling long reads. Good speed and sensitivity for RNA-seq analysis but with high memory usage. (https://github.com/alexdobin/STAR)
TMAP8 9 (Version 5.0.0) - Integrates a set of aligners to (including modified BWA) to identify candidate mapping locations and performs alignment using Smith-Waterman algorithm. TMAP is optimized to handle variable length reads and error profiles generated by Ion Torrent data. (https://github.com/iontorrent/TMAP)
TopHat9 10 (Version 1.4.1 with Bowtie 1.0.0) - Two stage aligner that first utilizes Bowtie to map to a reference and subsequently unaligned reads are are mapped to a database of possible splice junctions. Popular for RNAseq analysis with solid performance, speed, and memory usage. (https://ccb.jhu.edu/software/tophat/index.shtml)
TopHat 210 11 (Version 2.1.0) - A newer version of TopHat that utlizes Bowtie2 and refined algorithms from Tophat to improve both speed and accuracy. Popular for RNAseq analysis with solid performance, speed, and memory usage. (https://ccb.jhu.edu/software/tophat/index.shtml)
...
In addition, some aligners have additional options specific to that tool. BWA allows for selection of the Alignment algorithm, including backtrack, MEM and SW (see BWA documentation). GSNAP has multiple options for Alignment mode (see GSNAP documentation). Both TopHat and TopHat2 have the option to select Fusion search (see Fusion Gene Fusion Detection).
The Advanced options section allows for the customization of option sets (see Option Set Management), which allows for the ability to specify parameters specific to each aligner. Default parameters are those specified by the developer of each aligner and parameter details found in the documentation for each aligner.
...
5. Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinforma Oxf Engl. 2010;26(7):873-881.
6. Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015
7. Raczy C, Petrovski R, Saunders CT, et al. Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platforms. Bioinformatics. June 2013:btt314.
78. Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinforma Oxf Engl. 2013;29(1):15-21.
89. Torrent Suite User Documentation : Technical Note - TMAP Alignment (https://ts-pgm.epigenetic.ru/ion-docs/Technical-Note---TMAP-Alignment_9012907.html).
910. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinforma Oxf Engl. 2009;25(9):1105-1111.
1011. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
...
Overview
Content Tools