ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1585 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt1574 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...etic trees in cancer. SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.1416 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
...2 workflow identifies and verifiably removes primers on both ends of each ITS read, a key step due to the variable length of the ITS region. Short demonstrations of assign...1287 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
...ern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and...1247 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
...viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. https://academic.oup....1062 days ago
QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external softw...1011 days ago
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The complete sequence of a human genome
The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.780 days ago