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teagenomedata

teanalysis

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.

tea_dispensable_genome

termgraph

a python command-line tool which draws basic graphs in the terminal

tf_collaborativenet

tomatosuperpangenome

Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

tophat

Spliced read mapper for RNA-Seq

transdecoder

TransDecoder source

transrate

Understand your transcriptome assembly

trash

RepeatIdentifier

trim-aln

Performs basic alignment trimming

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

trinity_unigene

Filter longest trinity transcript as unigene

trinotate.github.io

web documentation for Trinotate

triobinningscripts

Scripts to reproduce TrioBinning manuscript

ts

Torrent Suite

unicycler

hybrid assembly pipeline for bacterial genomes

unifrac

urmap

URMAP ultra-fast read mapper

vcf-annotation-tools

A set of tools to annotate VCF files with expression and readcount data

vcf-miner

VCF-Miner: A graphical user interface for sorting, filtering and querying annotated VCF Files

vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA

vcf2hap

Construct gene haplotype with VCF format files and snpEff annotation.

vcf2phylip

Convert SNPs in VCF format to PHYLIP for phylogenetic analysis

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

vennerable

Vennerable provides Venn diagrams in R. It displays Venn and Euler diagrams for up to 9 different sets and using a variety of geometries. It allows the display of area-weighted Venn diagrams and allows fine graphical control over the result.

vennpainter

A tool for the comparison and identification of candidate genes based on Venn diagrams

veusz

Veusz scientific plotting application

veusz.github.io

github pages repository