Results for "GFA"
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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...1957 days ago
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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.gfa2363 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...1580 days ago
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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...2343 days ago
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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
1580 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequ...Tags: GfaViz, flexible, interactive, visualization, GFA, sequence, graphs
1576 days ago
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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-...809 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.1580 days ago
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