Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-s...nielnavarrogomez/phy-mer LAVA Genotyping of known SNPs (dbSNP and Affymetrix's Genom...fication and estimation of phylogenetic trees using SNPs (based on k-mer analysis...2369 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several ho...2329 days ago
Some useful Bioinformatics links
Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Ac...s/PMC4083407/ GATB/DiscoSnp: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as...2239 days ago
Tools to Predict the Impact of Missense Variants !
Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A...2201 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the specifi...-p nucmer assembly.fasta racon_assembly.fasta show-snps -C -T -r nucmer.delta This...de indels with the -I option in show-snps. This process (Racon -...2108 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencin...crucially on the accurate calling of SNPs and genotypes. Recently devel...eagle.html Multi-sample LD Candidate SNPs, genotype likelihoods Softwar...te_v2.html Multi-sample LD Candidate SNPs, genotype likelihoods Softwar...2094 days ago