Comment on "LAMSA: fast split read alignment with long approximate matches"
➜ LAMSA git:(master) ./lamsa aln Usage: lamsa aln [options] <ref.fa> <read.fa/fq> Algorithm options: -t --thread [INT] Number of threads. [1] -l --seed-len [...2136 days ago
2136 days ago
Comment on "SPAdes hybrid genome assembly"
use SPAdes to assemble the data. SPAdes is a swiss-army knife of genome assembly tools, and by default includes read correction. This takes up lots of RAM...2188 days ago
Comment on "Basic command-line to run BLAST"
Thanks for this blog ... here is some reference for BOL users urbe@urbo214b[Human_vs_Avaga_protein] wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/protein/protein.fa...2258 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
urbe@urbo214b[genome] graphmap align -h []GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapperGraphMap Version: v0.5.2Build date: Jun 6 2017...2306 days ago
Comment on "RACA: Reference-Assisted Chromosome Assembly"
Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genom...2785 days ago
Comment on "Software packages for next gen sequence analysis"
...assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data MaGuS (Map-GUided Scaffolding) is a scaffolder and a reference-free evaluator of assembly quality...2922 days ago
Comment on "Next generation sequencing in R or bioconductor environment"
We generally receive some common question like ... where to find human reference genome? What is reference annotation, how to download it etc. Here are some resources that...3634 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
r2cat (related reference based contig arrangement tool) can be used to order a set of contigs with respect to a single reference genome. This is done by mapping the contigs...3688 days ago
Comment on "List of popular bioinformatics software/tools"
EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing. http://epiexplorer.mpi-inf.mpg.de/3695 days ago