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 testing1913 days ago
GMASS: a novel measure for genomeassembly structural similarity
The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-z1860 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
...quence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal form...1660 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth...ld for each chromosome and genome-wide.quantized output that merges adjacent bases as...in the same coverage bins e.g. (10-20)threshold output to indicate how many bases in...1644 days ago
1609 days ago
StringTie Transcript assembly and quantification for RNA-Seq
...f longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specializ...1439 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
...aph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive...1595 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performa...1576 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...s Optional -k INT: kmer_length (<=32, default: 23) -od STRING: output_file_directory (default: ./)...of program but affects the memory usage (default: 100000000) -stdout: output the corrected reads to stdout...1564 days ago
1562 days ago