UPhO: Scripts for homology and orthology assessment from genomic sequences.
UPhO finds orthologs with and without inparalogs from input gene family trees. R...haracter "|" but custom delimiters can be defined. Examples of trees to test UPhO are provided in the TestData folder.1942 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible...1607 days ago
mutatrix: a population genome simulator which generates simulated genomes.
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.fasta1563 days ago
truvari: Structural variant comparison tool for VCFs
Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation1408 days ago
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URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2&tim...1287 days ago
COVID Moonshot: An international effort to DISCOVER A COVID ANTIVIRAL
The COVID Moonshot is an ambitious crowdsourced initiative to accelerate the...to determine which drug designs to send to our partners to make and test in the lab. With each drug design tested, we get closer to our goal....1236 days ago
RNA-Seq differential expression work flow using DESeq2
One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.990 days ago
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish inde...e by different alignment tools and provides a promising foundation on which to test new alignment ideas over larg...749 days ago
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