2151 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorith...2185 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
...romosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the d...1849 days ago
2173 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align...2171 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...Goris et al. 2007. However, it avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity estim...2121 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...d increasing accuracy of results by only considering those reads which should assemble together. Reducing/removing reference bias as compared to mapping based approaches. The soft...2109 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/nanofilt2105 days ago
2089 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-corrected reads have the highest mapping rate among all competing algo...2084 days ago