Comment on "LAMSA: fast split read alignment with long approximate matches"
...Read options: -e --err-rate [FLOAT] Maximum error rate of read. [0.04] -d --diff-rate [FLOAT] Maximum length difference ratio between read and reference. [0.04] -x --mis-rate [FLOAT]...2117 days ago
2117 days ago
Comment on "SPAdes hybrid genome assembly"
...amtools faidx SPAdes_hybrid/contigs.fasta NODE_1_length_4620446_cov_135.169_ID_22238 > single_contig.fa Finally, a quick comparison to the reference: sudo apt-get install mumm...2168 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.gz--2018-03...2238 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...Usage: graphmap [options] -r <reference_file> -d <reads_file>...tions: -r, --ref STR Path to the reference sequence (fastq or fasta). -i...ld only the index from the given reference and exit. If not specified, i...Normal alignment of reads to the reference. (Currently no other options...2286 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 genome of a closely related s...2765 days ago
Comment on "Software packages for next gen sequence analysis"
...ty 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 qu...2902 days ago
Comment on "Next generation sequencing in R or bioconductor environment"
...on question like ... where to find human reference genome? What is reference annotation, how to download i...e.ncbi.nih.gov/1000genomes/ftp/technical/reference/ftp://ftp.ncbi.nlm.nih.gov/ge...cse.ucsc.edu/goldenPath/hg19/chromosomes/Reference annotation downloadhttp://use...3615 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 onto the reference using a q-gram filter. The ma...3668 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/3676 days ago