snakepipes: A toolkit based on snakemake and python for analysis of NGS data
...re 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 Bisulfite...1801 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), and...848 days ago
SciLifeLab tutorial for bioinformatics analysis !
...ril - Uppsala2016 April - Uppsala2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembly 2016 November - Uppsala2017 November - Uppsala RNA-seq course 2015 October - Uppsal...2209 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 transcri...2188 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...2188 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 autosomal and sex-linked genes (genes located...2166 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 tool aims to improve the completeness of both protein-coding and non-coding...2153 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contai...2182 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, compact, unambiguous, ea...2173 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...plice ref.fa rna-reads.fa > aln.sam # spliced long reads ./minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa...2145 days ago