RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo...2032 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.1998 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to b...1946 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...lescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads,...1759 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the a...1597 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome asse...1576 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...-2 seq_files_right: comma separated files for the second mate in the paired-end data sets -i seq_files_interleaved: comma sperated files for interleaved paired-end data sets Optional -k INT...1565 days ago
MEC: Contig Misassembly Correction
...andidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical ana...1565 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1551 days ago
HS3D: Homo Sapiens Splice Sites Dataset
HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give...1436 days ago