CANU genome assembly parameters !
...ining the sequences after correction and final trimming *.layout : file containing informations about read inclusion in the final assembly *.gfa : file containing the as...1943 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...input and outputs an assembly graph in the GFA format. Different from m...miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA:...asm/miniasm -f reads.fq reads.paf.gz > reads.gfa2349 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows...onveniently parse, edit and write GFA files. Complex operations suc...formed. A typical application of RGFA is the editing of a graph, to...ompleted using a script based on RGFA. https://github.com/ggonnell...1565 days ago
Run miniasm assembler on nanopore reads !
...ally by minimap) as input and outputs an assembly graph in the GFA format. Different from m...; Assemble with miniasm: miniasm -f ONT_A.fasta AONT.paf > AONT.gfa grep '^S' AONT.gfa |aw...2328 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is ...Tags: RGFA, powerful, convenient, handling, assembly, graphs, GFA
1565 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...actical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa awk ’/^S/{print “>”$2”\n”$3}’ miniasm.gfa > miniasm.fasta assembly-...794 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.1565 days ago