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FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...

gwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...

github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...

github.com - genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Yau Group are a new research group based at the Wellcome Trust Centre for Human Genetics and the Department of Statistics at the University of Oxford. Yau Group develops statistical and computational methods for the analysis of genomic datasets...

github.com - orthodotter -h -------------------------------------------------------------------------------- orthodotter - Plot orthologous genes on an oxford grid. -f <file> : input file, containing orthologous genes, default is stdin...

www.strand-ngs.com - Strand Life Sciences announces the release of Strand NGS v3.1 at ASHG 2017 ORLANDO, USA, Oct 17, 2017/ PRNewswire/ Strand NGS now supports large scale RNA- and small-RNA-Seq and Unique Molecular Identifiers (UMIs) for DNA-, RNA-, and...

Calling narrow and broad peaks from ChIP-Seq data

A disease is considered to be ‘rare’ when it affects one in about 2000 individuals in the population. This, individually are although rare, collectively, the incidence could be very high causing a significant socio-economic burden....

When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the...