Comment on "A quick guide to Phred scaling"
Phred scaling is a widely used system for representing the quality scores of sequencing reads. It is used to quantify the probability of an error in...470 days ago
Comment on "Short-read assembly using Spades !"
Short-read assembly is the process of constructing a genome sequence from a large number of short sequencing reads. SPAdes (St. Petersburg genome ass...470 days ago
470 days ago
Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, IonTorrent, PacBio...476 days ago
Comment on "CovCal: Coverage / Read Count Calculator"
Sequencing coverage is defined as the average number of reads that covers each base of the reference genome. Estimating the sequencing coverage is very im...638 days ago
Comment on "Far Manager Commands and Links !"
KeyDescription F1 Yes! Read it first. BTW, FarEng.hlf is a simple text file, you can open it in any editor. ShiftF1 Create new archive fr...1016 days ago
Comment on "List of non-commercial NGS genotype-calling software"
Delly – Structural variant discovery by integrated paired-end and split-read analysis. [ paper-2012 ] lumpy – lumpy: a general probabili...1197 days ago
Comment on "URMAP, an ultra-fast read mapper"
map command Maps unpaired reads to a reference genome. The reference genome is stored as a UFI file created by the make_ufi command. The original FASTA file for th...1338 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
Using KAT again (You will need the modules: KAT/2.1.1 and gnuplot/4.6.5) – we can plot the kmer content of the assembly compared to the kmer content...1392 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
... <assembler>_perfect. This should take about a minute. The next tool we need is reapr smaltmap which creates a bam file of read-pair mappings. Do the same thing y...1392 days ago