Results for "assembly"
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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...405 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...410 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...786 days ago
Comment on "Genome assembly training tutorial at Galaxy !"
Understandinng genome assembly processes https://academic.oup.com/bfg/article/15/1/1/1741842943 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...1327 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...1327 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/26/4/570/2433691415 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/15/1/1/17418421521 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.png1539 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.1557 days ago
