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...429 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...429 days ago
429 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...435 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...597 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...975 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...1156 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...1297 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...1351 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...1351 days ago