snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C...1795 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), a...842 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences...2016 November - Uppsala2017 November - Uppsala RNA-seq course 2015 October - Uppsal...Uppsala2017 March - Uppsala2017 November - UppsalaRNAseq tutorials R Programming Foun...2203 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transc...2182 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer auto...How does SEX-DETector work? SEX-DETector does not require prior sequencing of a reference genome:...2160 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generatin...ach of which contains thousands of sparsely sequenced long fragments ranging...FJ, Shendure J#. In vitro, long-range sequence information for de novo...2176 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference gen...ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa...2139 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms...rforming transcriptome assembly from high-throughput sequencing data, they are very me...ms and expression levels while utilizing as many RNA-Seq libraries as possible that co...2126 days ago
2126 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types...e exists for a species for which an RNAseq experiment is performed. It a...ng de novo approaches. This type of RNAseq is as much of an art as well...the Reference genome-based type of RNA seq. http://chagall.med.cornel...2126 days ago