SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. Courses Old courses (2012-2014) Metagenomics Wor...2224 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construc...ties per "locus", including genome-aligned and gene-transcript aligned (genome-free) l...2203 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate th...2182 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
This software is provided ``as is” without warranty of any kind. In no event shall the author be held respo...e, including source codes, executables, and this documentation, is distributed free of...2197 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and go...good ability to handle various categories of SVs. LAMSA is open source and free fo...2196 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a spec...ly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free -...2147 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pa...2137 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for...1443 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free co...2082 days ago
STRUM: structure-based prediction of protein stability changes upon single-point mutation
STRUM is a method for predicting the fold stability change (ΔΔG) of protein molecules upon single-poi...ations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-en...2078 days ago