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 postprocess alignments. Sorted...1551 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/1464 days ago
SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
...files to run: The simplified gff file that was used as an input for a McScanX query. The collinearity file generated as an output by McScanX for the same input...1448 days ago
proActiv: Estimation of Promoter Activity from RNA-Seq data
...r activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to i...1374 days ago
1299 days ago
OGDRAW - Draw Organelle Genome Maps
...GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types...956 days ago
UniqueKmer: Generate unique KMERs for every contig in a FASTA file
...ard and reverse strands). This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig. The output unique k-mer file and Genome...883 days ago
835 days ago
Quip: Aggressive compression of FASTQ, SAM and BAM files.
...e space we take up and decrease data transfer times Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and&nb...725 days ago
JBrowse 2: a modular genome browser with views of synteny and structural variation
igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (wh...388 days ago