Comment on "Short-read assembly using Spades !"
Short-read assembly is the process of constructin...software tool for short-read assembly. Here are the general steps for short-read assembly using SPAdes: Quality co...repeated until a satisfactory assembly is achieved. These are t...442 days ago
Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg g...er) is a popular tool for short-read assembly. It can assemble reads genera...of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes...vides several options for tuning the assembly parameters, such as adjusting...447 days ago
Comment on "Run miniasm assembler on nanopore reads !"
minimap2 –x ava-ont \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fast...ldquo;>”$2”\n”$3}’ miniasm.gfa > miniasm.fasta assembly-stats ./miniasm.fasta dnadif...823 days ago
Comment on "Genome assembly training tutorial at Galaxy !"
Understandinng genome assembly processes https://academic.oup.com/bfg/article/15/1/1/1741842980 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:&...we can plot the kmer content of the assembly compared to the kmer content...n between the combined reads and the assembly. Make sure that you use the f...uo;noise” is part of the final assembly? What do you think contamina...1364 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
Reapr is a tool trying to find explicit errors in the assembly based on incongruently mapped...ommand reapr facheck <assembly.fasta> will tell you..., called 04.break.broken_assembly.fa. Use this file together wi...1364 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
Synteny based tool to arrange contigs "r2cat: synteny plots and comparative assembly" http://bibiserv.techfak.uni-bielefeld.de/r2cat https://academic.oup.com/bioinformatics/article/26/4/570/2433691452 days ago
Comment on "Genome assembly tutorial "Genome Assembly for short and long reads""
Do it yourself guide to genome assembly https://academic.oup.com/bfg/article/15/1/1/17418421558 days ago
Comment on "Bioinformatics tools developed for Oxford Nanopore data analysis !"
Basic commands for genome assembly https://raw.githubusercontent.com/rrwick/Long-read-assembler-comparison/master/supplementary_figures/Fig_S04_commands.png1576 days ago
Comment on "RGFA: powerful and convenient handling of assembly graphs"
The Graphical Fragment Assembly (GFA) is a proposed format which allow to describe the product of sequence assembly. This gem implements the proposed specifications for the GFA format described under https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md as close as possible.1594 days ago