Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...e erroneous long reads are corrected using the short reads. Current approaches rel...machine learning algorithms that address these shortcomings have the potential to...the basepairs of a long read are covered with short reads. Availability: Hercul...2100 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...mes, both prokaryotic and eukaryotic. However, short reads are difficult to assemb...d approaches that leverage the high quality of short reads to correct errors in lo...is based on two novel ideas: using a classical shortest path algorithm to find a s...2100 days ago
LRCstats: a tool for evaluating long reads correction methods
...downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next gener...2098 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
...size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple short read files. Removed use of c...2083 days ago
2055 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced...2040 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
...m reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads.&nbs...2034 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
...ta. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (usi...2034 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2000 days ago
Versatile genome assembly evaluation with QUAST-LG
...tarting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command! A short list of the new features (see...1976 days ago