NanoPack: visualizing and processing long-read sequencing data
...the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. https://academi...2108 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath I...ld like to use multiple threads, then the following commands can generate 20 threads to r...ontigs.fasta or raw_reads.fasta using the following comm...2099 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set...2081 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality cont...2077 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
...al selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming lan...2054 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
...ication with a graphical user interface, that can also be executed via command line. CSBFinder implements a nove...y for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - gr...2033 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...ach of these programs are included with the Synima package, and a pipeline for their use. Synima has a rang...nima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and p...2028 days ago
BamView: a free interactive display of read alignments in BAM data files
...: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is u...w.jar -h BAM files can be specified on the command line with the '-a' option: java -....bam If a BAM filename is not given on the command line BamView will prompt f...2017 days ago
2017 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was...LAST or NCBI BLAST. A fairly complete on-line guide to BLAST searching can...ult = 3 default = 11 Max scores:Number of one-line descriptions (V) [Integer] d...1987 days ago