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...1958 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.gfa2364 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...1581 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...2344 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-...810 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.1581 days ago