Results for "contigs"
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Comment on "Short-read assembly using Spades !"
...tput_dir> with the name of the output directory where the assembled contigs will be saved. Check the o...des has finished running, check the output directory for the assembled contigs. The contigs will be saved in...425 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...to each other. The program will also break up contigs/scaffolds at spurious sites to form smaller (but hopefully correct) contigs. Reapr runs pretty slowly, sa...nd you will get an assembly file with renamed contigs. Once the names are ok, we c...1341 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
Synteny based tool to arrange contigs "r2cat: synteny plots and comparative assembly" http://bibiserv.techfak.uni-bielefeld.de/r2cat https://academic.oup.com/bioinformatics/article/26/4/570/2433691430 days ago
Comment on "HALC: High throughput algorithm for long read error correction"
Inputs Long reads in FASTA format. Contigs assembled from the corresponding short reads in F...>short_reads.fa). Using AlignGraph runHALC.py long_reads.fa contigs.fa [-options|-options]...2096 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...fa > 20170918_oly_pacbio_miniasm_reads.fasta 4 Run minimap with default settings Using the default settings maps the FASTQ reads back to the contigs (the PAF file) created in the...2171 days ago
Comment on "SPAdes hybrid genome assembly"
...minion.pass.2D.fastq -o SPAdes_hybrid & Use samtools to extract the top contig: head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_...2178 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...z > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$2"\n"$3}' reads.gfa | fold > reads.fa And then count how many contigs: grep ">" reads.fa |...2179 days ago
- ...sembly. To run SPAdes we will use the spades.py command with the --careful option to minimize the number of mismatches in the contigs, -o for the output...
2348 days ago
Comment on "RACA: Reference-Assisted Chromosome Assembly"
Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a clos...2775 days ago
- ...graph. Second, the order of contigs is determined according to pa...----------- Constructs contigs using the algorithm based on...want to extend contigs at the cost of accuracy, set...If adjacent contigs have overlap (length >= IN...
2803 days ago
