Genetics

Qiime2

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.

OrthoFinder

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"

HISAT2

From the HISAT webpage:

STAR

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

RECON

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.

DIAMOND

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."

MetAMOS

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."

Pilon

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

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

SPAdes

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

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