QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline.


From the OrthoFinder website:

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"


From the HISAT webpage:


Spliced Transcripts Alignment to a Reference (STAR) is a software package developed for aligning large RNA-seq datasets.


RECON is software for automated de novo identification of repeat families from genomic sequences.


This software was originally developed by the Eddy lab. A newer version that fixes several bugs is available from the RepeatMasker webpage.


From the DIAMOND website:

"DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity."


From the MetAMOS website:

"MetAMOS represents a focused effort to create automated, reproducible, traceable assembly & analysis infused with current best practices and state-of-the-art methods. MetAMOS for input can start with next-generation sequencing reads or assemblies, and as output, produces: assembly reports, genomic scaffolds, open-reading frames, variant motifs, taxonomic or functional annotations, Krona charts and HTML report."


From the Pilon documentation:

"Pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies as well as call variants."


Funannotate is a pipeline for genome annotation originally designed for use with fungi genomes, but it can also be applied for other eukaryotes.


SPAdes  (St. Petersburg genome assembler) is an assembly toolkit with a variety of assembly pipelines.