Search Results for "miarma-seq"

kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. ...

The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in the following paper: Yang Liao, Gordon K Smyth and Wei Shi. "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote", Nucleic Acids Research, 2013, 41(10):e108

Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets.

The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.

lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/

SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. ...

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons.

QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).

MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/

MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/

SIPeS - Site Identification from Paired-end Sequencing