1932 days ago
1931 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment,...1868 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algori...PI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.1761 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects d...solving complex genomic regions. As a leading model organism with small genome size and great biotechnological im...1714 days ago
1688 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A...1656 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV cal...1631 days ago
heatmaply: popular graphical method for visualizing high-dimensional data
This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to z...1576 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file...pped bases. Both values are subjected to the genome size estimation. Providing accurat...1570 days ago