FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedF...like to use multiple threads, then the following commands can generate 20 threads to r...igs.fasta or raw_reads.fasta using the following command. perl -pe 's/>[^\$]*$...2106 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...2088 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 c...2084 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
...cial 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 programmin...2061 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the disco...2040 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...abels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative...2035 days ago
BamView: a free interactive display of read alignments in BAM data files
...IX: java -mx512m -jar BamView.jar and extra command line options are given when '...iew.jar -h BAM files can be specified on the command line with the '-a' option: j...ed.bam If a BAM filename is not given on the command line BamView will prompt for...2025 days ago
2024 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
...aphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrat...1992 days ago
1986 days ago