Synima: a Synteny imaging tool for annotated genome assemblies
...size, colours, order, and labels, which are specified in a config file generated by the first run of Synima &...d can be subsequently edited. Synima runs quickly on a command line to generate informative and publication q...2069 days ago
1994 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
...al errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing b...1983 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing1955 days ago
The Extensive de novo TE Annotator (EDTA)
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of in...1787 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
...suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data....1775 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we e...1699 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...ycles. Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs. https://a...1614 days ago
pbmm2:A minimap2 frontend for PacBio native data formats
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and...1593 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
...uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. O...all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of conti...1517 days ago