jtools : more efficient presentation of regression analyses
This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the...1603 days ago
1558 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.1524 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identit...git clone https://github.com/rrwick/Filtlong.git cd Filtlong make -j bi...1511 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive d...ts to find the bridging that cross the gap, and then fills the long read original sequence into t...1510 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both k...1506 days ago
1345 days ago
Updated science-wide author databases of standardized citation indicators
.... Accordingly, we have provided updated analyses that use citations from Scopus with data freeze as of May 6, 2020, assessing scientists for career-long citation impact up until the...1325 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
...PU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Descr...1291 days ago
maftools : Summarize, Analyze and Visualize MAF Files
...package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner from either TCGA sources or any in-house studies as long as the data is in MAF format.1288 days ago