funannotate: Eukaryotic Genome Annotation Pipeline
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes),...2052 days ago
2044 days ago
MITOS: improved de novo metazoan mitochondrial genome annotation
Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows...2015 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...thoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a r...2011 days ago
2005 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...package and has been proved to be scalable, so that its allows the study of very large datasets. SiLiX is already included in the analysis pipeline for HOGENOM....1968 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1967 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...igs that are syntenic and move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and...etermine the proper assignment of any remaining ambiguous contigs. The pipeline will run on either a haploid...1963 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
...es together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps:&...1960 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmot...1936 days ago