2354 days ago
Ribbon: Visualizing complex genome alignments and structural variation:
Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab...2354 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse taxo...s present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a&n...2349 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
...ed Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We e...our tool on 30× simulated pair-end reads from Arabidopsis thaliana wit...tool FLASH. When COPE is applied to real reads for genome assembly, the resu...2347 days ago
2340 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2338 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
...s serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome....2335 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed u...2331 days ago
2326 days ago
Seal: SEquence ALignment evaluation suite
...gth, repeat count, repeat length, repeat variability rate). Simulating reads from random locations in the...r rate, and indel rate. Applying alignment tools to the genome and the reads through a standardized interf...2319 days ago