NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based...2057 days ago
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but p...nment parameters depending on the reads and application. lordFAST,...igned to align reads generated by PacBio and...2045 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2044 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as pro...s between the segments (like Artemis, for example) Reads from...2030 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes cont...em to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignme...ced for all flagged contig matches, juxtaposed with read-cover...2026 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)2025 days ago
NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with...2017 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determin...ng paradigm that enhances the correction policy at each iteration by i...nce metrics assigned to prior corrections.2010 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read align...2009 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
kallisto is a program for quantifying abundances of transcripts fro...nces using high-throughput sequencing reads. It is based on the novel id...idly determining the compatibility of reads with targets, without the ne...a Mac desktop computer using only the read seque...2004 days ago