Comment on "Short-read assembly using Spades !"
...software tool for short-read assembly. Here are the general steps for short-read assembly using SPAdes: Quality co...TQ format. Evaluation of assembly: After running SPAdes, the ne...repeated until a satisfactory assembly is achieved. These are t...554 days ago
Comment on "Short-read assembly using Spades !"
...e assembler) is a popular tool for short-read assembly. It can assemble reads genera...overview of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes...also provides several options for tuning the assembly parameters, such as adjusting...559 days ago
Comment on "Run miniasm assembler on nanopore reads !"
..../minimap.paf.gz > miniasm.gfa awk ’/^S/{print “>”$2”\n”$3}’ miniasm.gfa > miniasm.fasta assembly-stats ./miniasm.fasta dnadif...935 days ago
Comment on "Genome assembly training tutorial at Galaxy !"
Understandinng genome assembly processes https://academic.oup.com/bfg/article/15/1/1/17418421091 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...) – we can plot the kmer content of the assembly compared to the kmer content...comparison between the combined reads and the assembly. Make sure that you use the f...kmer “noise” is part of the final assembly? What do you think contamina...1475 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...g to find explicit errors in the assembly based on incongruently mapped...e command reapr facheck <assembly.fasta> will tell you...lems, run reapr facheck <assembly.fasta> <renamed_assembl...ile, called 04.break.broken_assembly.fa. Use this file together wi...1475 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/26/4/570/2433691564 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/15/1/1/17418421670 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.png1688 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.1706 days ago