transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in det...2182 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nucl...ence mapping engine to compute the orthologous mappings...plications are described here: "High-throughput ANI Analysis of 90K Prokaryotic Genomes Re...2182 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and...2169 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, referenc...;assemblies with the intent of: Reducing time in analysis and increasing accuracy o...' contained within next-generation shotgun sequence data. ARC decomplexifies the tradition...2169 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/nanofilt2165 days ago
LSC :a long read error correction tool
Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the&nbs...;tutorial to see how LSC works on some example data. Read the manual if an...2162 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline t...m SV calling from low coverage long-read sequencing data. NextSV integrates three alig...rated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV...2158 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for...r patterns, annotations and rarefraction curve analysis. The most basic analysis only...patible xhtml to visualize/share/store/extract analysis results. https://f1000resear...2157 days ago
2157 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleot...ic status and clonality. PureCN is designed for targeted short read sequencing data, in...2155 days ago