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Diffstat (limited to 'academic/ugene/README')
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1 files changed, 9 insertions, 5 deletions
diff --git a/academic/ugene/README b/academic/ugene/README index ef532fe350..515ecec210 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -35,7 +35,7 @@ program. All of them are available at SlackBuilds.org: - bedGraphToBigWig (Convert bedGraph to bigWig file) - bedtools (A powerful toolset for genome arithmetic) - bowtie (A short read aligner of DNA sequences) -- bowtie2 (A tool for aligning sequencing reads) +- bowtie2-legacy (A tool for aligning sequencing reads) - bwa (Burrows-Wheeler Aligner) - cap3 (CAP3: A DNA sequence assembly program) - cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) @@ -43,23 +43,27 @@ program. All of them are available at SlackBuilds.org: - cistrome-extra (Cistrome Applications Harvard extra apps) - cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) - cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos) +- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - cutadapt (Trim adapters from high-throughput sequencing reads) +- diamond (A sequence aligner for protein and translated DNA) - fastqc (A quality control tool for high throughput sequence data) - HMMER (Biosequence analysis using profile hidden Markov models) +- kraken (Assign taxonomic labels to short DNA sequences) - ncbi-blast (BLAST: Basic Local Alignment Search Tool) -- ncbi-blast-plus (BLAST+ Command Line Applications) +- ncbi-blast+ (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) -- samtools (Sequence Alignment/Map Tools) +- samtools-legacy (Sequence Alignment/Map Tools) - snpEff (Genetic variant annotation and effect prediction toolbox) - spades (SPAdes Genome Assembler) - spidey (mRNA-to-genomic alignment) - t_coffee (A multiple sequence alignment program) -- tabix (Generic indexer for TAB-delimited genome position files ) +- tabix-legacy (Generic indexer for TAB-delimited genome position files ) - tophat (Splice junction mapper for RNA-Seq reads) +- trimmomatic (A flexible read trimming tool for Illumina NGS data) - vcftools (A program package designed for working with VCF files) Alternatively, check the program's website if you want to get them -precompiled: http://ugene.net/external.html +precompiled. |