mScaffolder: A comparative genome scaffolding tool
...sing an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guide...2163 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...Bio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and the...ijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their...2142 days ago
transrate: Understanding your transcriptome assembly
...al evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help de...2135 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
...sing the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ -ds alternative...2122 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
...destinedFolder mummerPath Sometimes, if the names of raw reads and contigs consists of special character...ectly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw...2097 days ago
2052 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
...d paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.2037 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the...2037 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
...assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy....2037 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...ee of heterozygosity. This causes contigs for both haplotypes of that p...be assembled as separate primary contigs, rather than as a contig and...loid assembly. Identify pairs of contigs that are syntenic and move on...gnment of any remaining ambiguous contigs. The pipeline will run on eit...1978 days ago