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PANDASeq.is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
(Improving the quality) (Quality control, trimming, error correction and pre-processing of data) -
WGsim Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms. (RNA-Seq simulators)
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RNA-Seq Atlas a reference database for gene expression profiling in normal tissue by next-generation sequencing.
(Human related) (RNA-Seq databases) -
SplicePie is a pipeline to analyze non-sequential and multi-step splicing. SplicePie contains three major analysis steps: analyzing the order of splicing per sample, looking for recursive splicing events per sample and summarizing predicted recursive splicing events for all analyzed sample (it is recommended to use more samples for higher reliability). The first two steps are performed individually on each sample and the last step looks at the overlap in all samples. However, the analysis can be run on one sample as well.
(General tools) (Alternative splicing analysis) -
IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR is an R package that enables statistical identification of isoform switches with predicted functional consequences where the consequences of interest can be chosen from a long list but includes gain/loss of protein domains, signal peptides changes in NMD sensitivity. IsoformSwitchAnalyzeR is made for post analysis of data from any full length isoform/transcript quantification tool but directly support Cufflinks/Cuffdiff, RSEM Kallisto and Salmon.
(Differential isoform/transcript usage) (Alternative splicing analysis) -
BreakFusion (Fusion genes/chimeras/translocation finders/structural variations)
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