2347 days ago
2319 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
...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 Whole Genome Bisul...1800 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
...synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other species identifie...bsp; Species Assembly Code Transcriptome lncRNAs Protein-coding...846 days ago
SciLifeLab tutorial for bioinformatics analysis !
...De Novo Genome Assembly 2016 November - Uppsala2017 November - Uppsala RNA-seq course 2015 October - Up...Uppsala2016 October - Uppsala2017 March - Uppsala2017 November - UppsalaRNAseq tutorials R Programming F...2208 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...2187 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single refere...2187 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This...of both protein-coding genes and circular RNAs were almost completely recov...cially for long proteins and long circular RNAs.2151 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise,...ch such structural feature. The bpRNA code is written in perl and r...at http://github.com/hendrixlab/bpRNA....2172 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
....sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam #...map2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1...2143 days ago