gencore_annotation
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
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
freebayes
Version: 1.0.2.29
Conda Channel: bioconda
Summary:
Bayesian haplotype-based polymorphism discovery and genotyping
genblasta
Version: 1.0.4
Conda Channel: bioconda
Summary:
genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.
genblastg
Version: 1.38
Conda Channel: bioconda
Summary:
genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.
hmmer
Version: 3.1b2
Conda Channel: bioconda
Summary:
Biosequence analysis using profile hidden Markov models
jellyfish
Version: 2.2.3
Conda Channel: bioconda
Summary:
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
kat
Version: 2.0.8
Conda Channel: bioconda
Summary:
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts
kmergenie
Version: 1.7016
Conda Channel: bioconda
Summary:
KmerGenie estimates the best k-mer length for genome de novo assembly
pauda
Version: 1.0.1
Conda Channel: bioconda
Summary:
perl-app-cpanminus
Version: latest
Conda Channel: bioconda
Summary:
get, unpack, build and install modules from CPAN
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:
repeatmasker
Version: 4.0.6
Conda Channel: bioconda
Summary:
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
rmblast
Version: 2.2.28
Conda Channel: bioconda
Summary:
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.
samtools
Version: 1.3.1
Conda Channel: bioconda
Summary:
Tools for dealing with SAM, BAM and CRAM files
snpeff
Version: 4.3
Conda Channel: bioconda
Summary:
Genetic variant annotation and effect prediction toolbox
tophat
Version: 2.1.0
Conda Channel: bioconda
Summary:
A spliced read mapper for RNA-Seq
transdecoder
Version: 2.1.0
Conda Channel: bioconda
Summary:
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
trinotate
Version: 3.0.1
Conda Channel: bioconda
Summary:
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms
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.