BOL

neufeldserver.uwaterloo.ca - PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable...

Structural variation caller tools using long reads

shendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...

lindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...

github.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...

www.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...

amos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...

github.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...

github.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...