gencore_de_novo_genomic
Summary
Coming soon!
Software Packages
abyss
Version: 1.9.0
Conda Channel: bioconda
Summary:
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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
discovar
Version: 52488
Conda Channel: bioconda
Summary:
Suitable for variant calling with reference and de novo assembly of small genomes.
discovardenovo
Version: 52488
Conda Channel: bioconda
Summary:
Suitable for de novo assembly of large and small genomes.
freebayes
Version: 1.0.2.29
Conda Channel: bioconda
Summary:
Bayesian haplotype-based polymorphism discovery and genotyping
gatk
Version: 3.6
Conda Channel: bioconda
Summary:
The full Genome Analysis Toolkit (GATK) framework, license restricted.
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
idba
Version: 1.1.1
Conda Channel: bioconda
Summary:
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
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
kmergenie
Version: 1.7016
Conda Channel: bioconda
Summary:
KmerGenie estimates the best k-mer length for genome de novo assembly
mira
Version: 4.0.2
Conda Channel: bioconda
Summary:
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)
pear
Version: 0.9.6
Conda Channel: bioconda
Summary:
paired-end read merger
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:
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
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
spades
Version: 3.9.0
Conda Channel: bioconda
Summary:
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
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.
velvet
Version: 1.2.10
Conda Channel: bioconda
Summary:
Sequence Assembler for short reads