jobTree based python wrapper to run the genome simulation tool suite Evolver
evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution o...n and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extrac...2333 days ago
2329 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequ...es that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexe...2183 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative i...2156 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC alig...cies with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome re...2152 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error pattern...BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extrac...2092 days ago
S-plot2: creates an interactive, two-dimensional heatmap of sequences
...be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatm...is facilitates the investigation of quickly evolving coding regions, novel coding regions, and l...2040 days ago
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
...be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatm...is facilitates the investigation of quickly evolving coding regions, novel coding regions, and l...2035 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencin...ore efficient to store only those read-pairs or reads who intersect some region around the variant locations....2033 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) pe...2013 days ago