gencore_de_novo_transcriptome

Summary

Coming soon!

Software Packages

augustus

Version: 3.2.2

Conda Channel: bioconda

Summary:

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.

bamtools

Version: 2.4.0

Conda Channel: bioconda

Summary:

C++ API & command-line toolkit for working with BAM data

bcftools

Version: 1.3.1

Conda Channel: bioconda

Summary:

Tools for dealing with BCF and VCF files

bedtools

Version: 2.25.0

Conda Channel: bioconda

Summary:

A powerful toolset for genome arithmetic

bioconductor-deseq2

Version: 1.10.1

Conda Channel: bioconda

Summary:

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

bioconductor-deseq

Version: 1.22.1

Conda Channel: bioconda

Summary:

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

bioconductor-edger

Version: 3.14.0

Conda Channel: bioconda

Summary:

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

blast

Version: 2.2.31

Conda Channel: bioconda

Summary:

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

blat

Version: 35

Conda Channel: bioconda

Summary:

BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.

bowtie2

Version: 2.2.8

Conda Channel: bioconda

Summary:

Fast and sensitive read alignment

bwa

Version: 0.7.15

Conda Channel: bioconda

Summary:

The BWA read mapper.

circos

Version: 0.69.2

Conda Channel: bioconda

Summary:

Circos is a software package for visualizing data and information. It visualizes data in a circular layout

Version: 2.2.1

Conda Channel: bioconda

Summary:

Transcriptome assembly and differential expression analysis for RNA-Seq.

hmmer

Version: 3.1b2

Conda Channel: bioconda

Summary:

Biosequence analysis using profile hidden Markov models

htseq

Version: 0.6.1.post1

Conda Channel: bioconda

Summary:

A framework to process and analyze data from high-throughput sequencing (HTS) assays

pear

Version: 0.9.6

Conda Channel: bioconda

Summary:

paired-end read merger

perl-biox-workflow-plugin-filedetails

Version: 0.11

Conda Channel: bioconda

Summary:

Get metadata for files in directories processed by BioX::Workflow

perl-biox-workflow-plugin-fileexists

Version: 0.13

Conda Channel: bioconda

Summary:

a plugin to BioX::Workflow

perl-biox-workflow

Version: 1.10

Conda Channel: bioconda

Summary:

A very opinionated template based workflow writer.

perl-hpc-runner-command

Version: 3.1.1

Conda Channel: bioconda

Summary:

picard

Version: 2.5.0

Conda Channel: bioconda

Summary:

prinseq

Version: 0.20.4

Conda Channel: bioconda

Summary:

PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data

quast

Version: 4.1

Conda Channel: bioconda

Summary:

Quality Assessment Tool for Genome Assemblies

rsem

Version: 1.2.28

Conda Channel: bioconda

Summary:

RSEM (RNA-Seq by Expectation-Maximization)

salmon

Version: 0.6.0

Conda Channel: bioconda

Summary:

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

samtools

Version: 1.3.1

Conda Channel: bioconda

Summary:

Tools for dealing with SAM, BAM and CRAM files

seqtk

Version: 1.2

Conda Channel: bioconda

Summary:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

sickle

Version: 0.5

Conda Channel: bioconda

Summary:

A lightweight OAI client library for Python

star

Version: 2.5.2a

Conda Channel: bioconda

Summary:

An RNA-seq read aligner.

tophat

Version: 2.1.0

Conda Channel: bioconda

Summary:

A spliced read mapper for RNA-Seq

trimmomatic

Version: 0.36

Conda Channel: bioconda

Summary:

Genetic variant annotation and effect prediction toolbox

vcflib

Version: 1.0.0_rc1

Conda Channel: bioconda

Summary:

Command-line tools for manipulating VCF files

vcftools

Version: 0.1.14

Conda Channel: bioconda

Summary:

A set of tools written in Perl and C++ for working with VCF files.

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