ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...ce assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial sh...sassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences fr...2145 days ago
transrate: Understanding your transcriptome assembly
... transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for...2138 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently...1444 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...n analysis and increasing accuracy of results by only considering those reads which should assemble togethe...exifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subset...2125 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofilt2121 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs a...2040 days ago
2106 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
...unning on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python fi...you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads...2100 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...gth. Several studies require long and accurate reads including de novo assembly, f...both technologies and the more erroneous long reads are corrected using the short...read and uses this to correct errors in these reads. Using datasets from two DNA-...2100 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...tic and eukaryotic. However, short reads are difficult to assemble and...s. The recent developments in long reads sequencing methods offer a pr...leverage the high quality of short reads to correct errors in long rea...of unmapped mates of mapped short reads. Our results on bacterial, fu...2100 days ago