BOL

ccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...

github.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...

github.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....

crossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly...

easyfig.sourceforge.net - Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.  Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use...

bioinformatics.oxfordjournals.org - QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison. More...

http://busco.ezlab.org/ - High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures...

github.com - Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh Goal: To create blobplots or...

github.com - HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler...

ocw.mit.edu - https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf