GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryo...java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ -ds alternative_assemblies.fasta -ref reference.fasta \...2154 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
...ath If you are running on server computer and would like to use multiple threads, then the following c...to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command....2129 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focu...r randomly generated reference sequence. The reference can be read from a FASTA file or randomly generated wi...2127 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and evol...a novel method and a network server for comparing multiple draft and finished-quality se...ly conserved transcription factor binding sites in multi...2125 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative a...ads are further polished using long-distance dependencies that are found using multi...2112 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 proc...ter compressed intermediate files. Added utilities folder. Added support for multi...2112 days ago
2090 days ago
KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment
KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) a..., and generates annotations for each gene based on multiple databases about pathways, dis...nrichment and enrichment score based on results of multi...2069 days ago
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 multi...2063 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using...is fast, and produces an identical assembly for the same input when assembled multi...2043 days ago