Results for "gfa"
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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-...804 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.1575 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ome/data/20170911_oly_pacbio_cat.fastq /home/data/20170911_minimap2_pacbio_oly.paf > /home/data/20170918_oly_pacbio_miniasm_reads.gfa 3 Convert miniasm output GFA to FASTA The FASTA file is n...2175 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{prin...2183 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...fastq both.fastq[M::main] Real time: 3608.342 sec; CPU: 67037.124 securbe@urbo214b[allONT] ~/Tools/miniasm/miniasm -f both.fastq AONT.paf > AONT.gfa [][M::main] ===> Step 1: r...2289 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...ptions are: auto - Determines the format automatically from file extension. fastq - Loads FASTQ or FASTA files. fasta - Loads FASTQ or FASTA files. gfa - Graphical Fragment Assembly...2300 days ago
