BOL

Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...

broadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...

mira-assembler.sourceforge.net - MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion...

www.bioinformatics.babraham.ac.uk - Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...

sc932.github.io - Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and...

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...

Diploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference Genomes

The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p,...

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and...

github.com - In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who...