BOL: Results for "gfa"

Results for "gfa"

- Rahul Nayak@rahul
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...
1953 days ago

- Jit@jit.aber
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.gfa
2359 days ago
- Rahul Nayak@rahul
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...
1575 days ago
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- Jit@jit.aber
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...
2338 days ago

- Jit@jit.aber
#GFA to #FASTA file conversion. awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa
2289 days ago
- Jit@jit.aber
#GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa
2282 days ago

- Rahul Nayak@rahul
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-...
804 days ago
- Rahul Nayak@rahul
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.
1575 days ago
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