gencore_de_novo_metagenomic
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
hmmer
Version: 3.1b2
Conda Channel: bioconda
Summary:
Biosequence analysis using profile hidden Markov models
mawk
Version: 1.3.4
Conda Channel: bioconda
Summary:
mawk is an interpreter for the AWK Programming Language.
metaphlan2
Version: 2.5.0
Conda Channel: bioconda
Summary:
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
metavelvet-sl-feature-extraction
Version: 1.0
Conda Channel: bioconda
Summary:
Perl libraries that do feature extraction for metavelvet-sl
metavelvet-sl
Version: 1.0
Conda Channel: bioconda
Summary:
MetaVelvet-SL : An extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning
metavelvet
Version: 1.1.01
Conda Channel: bioconda
Summary:
MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
mothur
Version: 1.36.1
Conda Channel: bioconda
Summary:
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
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
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.