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Fast gapped-read alignment with Bowtie 2
Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy. Expand
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds. Expand
TopHat: discovering splice junctions with RNA-Seq
The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. Expand
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation. Expand
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
TopHat2 is described, which incorporates many significant enhancements to TopHat, and combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. Expand
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
This protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results, which takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time. Expand
HISAT: a fast spliced aligner with low memory requirements
Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory. Expand
FLASH: fast length adjustment of short reads to improve genome assemblies
FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. Expand
Versatile and open software for comparing large genomes
The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewingExpand
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts produces more complete and accurate reconstructions of genes and better estimates of expression levels. Expand