Results for "Genome Assembly"
Top-level pages
Gap filling or Contigs extensions tools !
...ook at the IMAGE tool: http://genomebiology.com/2010/11/4/R41...rested in assembling the full genome, just the 100 kb part you're in...1. Start with the initial assembly C0 of the contigs you have id...nd reads. c. Construct a new assembly C' from C and the new reads i...2162 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabula... 2. sseqid subject (e.g., reference genome)...2135 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the sp...o I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta n...2107 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extens...tp://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Multi-sample...r.ac.uk/resources/software/margarita) MaCH http://genome.s...2093 days ago
Bioinformatics in Africa:- Part 1
The Institut Pasteur de Côte d’Ivoire was created by the N°72511 l...training in bioinformatics and genome data analysis. Sho...7 a yearly regional course of initiation and using genome d...1186 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. Y...mina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina -1 i...822 days ago
Bioinformatics tools for genome assembly !
...is a list of some widely used genome assembly tools as of my last update...le for small and medium-sized genomes. Unicycler: A hybrid asse...for circular bacterial genome assembly. wtdbg2: A de Bruijn gra...constantly evolving, and new assembly tools may have emerged since...283 days ago
Steps to find all the repeats in the genome !
To find repeats in a genome from 2 to 9 length using a Perl script, you can use...he RepeatMasker website[0]. Prepare the genome sequence: Make sure you have the genome sequence in a FASTA file form...ecific needs and the characteristics of your genome....245 days ago
Mitochondrial genome assembly tools !
...making it an ideal target for assembly. Here are some commonly used mitochondrial genome assembly tools: MitoFinder: Mitofin...for annotating mitochondrial genomes. It integrates multiple softwa...PAdes: SPAdes (St. Petersburg genome assembler) is a versatile genom...239 days ago
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