BOL

github.com - GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two...

www.homolog.us - If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard...

github.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...

http://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...

abacas.sourceforge.net - ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly...

kakitone.github.io - FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...

chunlab.wordpress.com - CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes. To use CLgenomics, individual...

seqmule.openbioinformatics.org - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...

www.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...

gehlenborglab.shinyapps.io - UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such...