github.com - genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms
More at https://github.com/ekg/mutatrix
./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta
ecogenomics.github.io - CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous...
github.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...
ftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...
code.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...
github.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...
bix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...
sourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads.
Cerulean v0.1 has been implemented with bacterial genomes in mind.
The method is fully described in...
github.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.
Headline Features:
Fast, smooth scrolling and zooming. Explore your genome with unparalleled...
