BOL

sourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...

In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.

ucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...

Ongoing research in the group of Karine Van Doninck involves topics at the core of evolutionary biology, including the evolution of sex, genome maintenance, recombination and extreme stress resistance on different eukaryotic systems, including...

Bioinformatics tools

github.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

github.com - Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.  Depending on your genome size you may want to convert the .wig files to the BigWig format.

To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide: Install RepeatMasker: First, you need to install RepeatMasker on your system. You...

FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...

github.com - GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20...