github.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...
github.com - A probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...
1000 Genomes data tutorial at ASHG
Structural variants presentation by
Jan Korbel
European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research...
github.com - SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
More at
https://github.com/jts/sga
SGA...
github.com - MeGAMerge
MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
Description
MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...
bedtools.readthedocs.io - Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For...
code.google.com - splitbam splits a BAM by chromosomes.
Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...
www.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...
github.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...
www.ncbi.nlm.nih.gov - NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional...
