Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput...
www.ncbi.nlm.nih.gov - Install and use the NCBI Datasets command line tools
The NCBI Datasets datasets command line tools are datasets and dataformat .
Use datasets to download biological sequence data across all domains of life from...
github.com - bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and...
https://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...
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...
GABi Research
The major researching fields defined as the GABi scope are described next:
Sequence Analysis
Protein Structure Prediction
Comparative Genomics
Functional Analysis of Residues on Protein Families
Gene/Protein...
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...
wiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data
We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...
www.cs.utoronto.ca - With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly...