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,...
github.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Mads...
A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.
github.com - An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is...
github.com - KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT:
hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in...
github.com - The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.
EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single...
www.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...
sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly.
It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...