BOL

github.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...

Saved Cornell University assembly workshop PPT. Reference:  http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf

faculty.cse.tamu.edu - With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from...

github.com - 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 indels with respect to a reference genome...

github.com - Watch out: only a few files are counted in coverage statistics. Full documentation on Read the Docs. A set of tools for viral metagenomics. virmet is called with a command subcommand syntax: virmet fetch --viral n, for example,...

http://genomeribbon.com/ - Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in...

Choose the appropriate parameters to run Canu and run it.

faculty.washington.edu - Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and...

eforge.cs.ucl.ac.uk - The eFORGE tool provides a method to view the tissue specific regulatory component of a set of EWAS DMPs. eFORGE analysis takes a set of DMPs, such as those hits above genome-wide significance threshold in an EWAS study, and analyses whether there...

www.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...