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
cufflinks
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.