ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a p...2382 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler fo...It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an asse...rial data sets. Including the mapping step, it takes about 3 mi.... It also shows that minimap&n...fastq reads.fq # Install minimap and...2378 days ago
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Frontend: Perl Web framework documentation - Andrej Sali Lab
The frontend is a set of Perl classes that displays the...frontend class must be subclassed for each web service. This class is then used to...eb pages using a set of CGI scripts that are set up automatically by the build system.2336 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and...lowing compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map rea...1565 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, includin...2211 days ago
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chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
Provides interactive, configurable and elegant graphics visualization of th...of any living organism allowing users to map chromosome elements (like gen...s a special plot viz. the "chromosome heatmap"...isualizing multiple sets, chromosome heat-maps, g...1878 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long seque...inst a reference genome ./minimap2 -a test/MT-human.fa test/MT-...ndex first and then map ./minimap2 -d MT-human.mmi test/MT-huma...genomic reads ./minimap2 -ax map-o...es asm-to-asm alignment ./minimap2 -x...2174 days ago