RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
...d to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS...1595 days ago
QuorUM: An Error Corrector for Illumina Reads
We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found th...1563 days ago
MEC: Contig Misassembly Correction
MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large numb...1563 days ago
SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:1554 days ago
SvABA: Structural variation and indel detection by local assembly
...g Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb...t of reads at the command line using VariantBam rules. These contigs are then immediately aligned...1529 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplet...1498 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/b...1460 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
...rmation from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly...1164 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...ample and matched sample scenarios. SVEngine takes as input reference contigs in FASTA files, variant meta...cifying clonal phylogenetic trees in cancer. SVEngine outpus alterred contigs in FASTA files, spiked-in var...1413 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
...shared, and can be inspected anywhere using a web interface. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot po...1369 days ago