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media-libs/libgfx
Simplify the creation of computer graphics software
media-libs/scifio-jai-imageio
SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core.
media-libs/imglib2
A multidimensional, type-agnostic image processing library.
media-libs/glbinding
Cross-platform C++ binding for the OpenGL API
media-libs/mmg
bidimensional and tridimensional remesher
media-gfx/brlcad
Constructive solid geometry modeling system
sci-biology/ANGLE-bin
CDS prediction overcoming sequencing errors in unfinished cDNA
sci-biology/FLASH
Paired-end mates merge from fragments
sci-biology/CAT
Codon usage bias (composition) and its statistical significance
sci-biology/IMAGE
Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina
sci-biology/LINKS
Scaffold genome assemblies by Chromium/PacBio/Nanopore reads
sci-biology/MaSuRCA
de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore
sci-biology/Rcorrector
Error correction for Illumina RNA-seq reads
sci-biology/RAILS
Cobbler and RAILS scaffolding tools acting on SAM streams
sci-biology/ParaAT
Create multiple protein-coding DNA alignments and back-Translation
sci-biology/SEECER
SEquence Error Corrector for RNA-Seq reads
sci-biology/SSAKE
Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers
sci-biology/TransDecoder
Extract ORF/CDS regions from FASTA sequences
sci-biology/VelvetOptimiser
Optimise Velvet sequence assembler
sci-biology/abacas
Order and orientate DNA contigs even via 6-frame protein alignments
sci-biology/afni-datasets
Datasets for using and testing sci-biology/afni
sci-biology/angsd
Population genetics analysis package
sci-biology/align_to_scf
View trace information at a given position missing from Roche .ace files
sci-biology/bedops
Manipulate BED file (alternative to bedtools)
sci-biology/biobambam2
Tools for bam file processing (libmaus2)
sci-biology/bismark
Map bisulfite converted sequence reads and cytosine methylation states
sci-biology/bru2nii
Converts Bruker ParaVision MRI data to the NIfTI file format
sci-biology/btl_bloomfilter
BTL C/C common bloom filters
sci-biology/cast-bin
Predict low-complexity regions in putative proteins
sci-biology/cdbfasta
FASTA record indexing/retrievieng utility
sci-biology/cluster
Hierarchical, k-means, k-medians clustering for expression/microarray analysis
sci-biology/cross_genome
Genome scaffolding using cross-species synteny
sci-biology/ffindex
Simple index/database for huge amounts of small files
sci-biology/fastdnaml
Maximum likelihood phylogenetic tree builder for DNA sequences
sci-biology/fsa
Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot
sci-biology/gffcompare
Compare, classify, merge, track, annotate GFF files
sci-biology/gffread
GFF/GTF utility providing format conversions, filter/extract regions from FASTA
sci-biology/jellyfish
k-mer counter within reads for assemblies
sci-biology/libBigWig
C library for handling bigWig files (functionally replacing Jim Kent's lib)
sci-biology/lumpy-sv
Probabilistic framework for structural variant discovery
sci-biology/lucy
DNA sequence quality and vector trimming tool
sci-biology/ntCard
Estimate k-mer coverage histogram of genomics data
sci-biology/nxtrim
Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
sci-biology/pairagon
HMM-based cDNA to genome aligner
sci-biology/parafly
Parallel cmd processing utility
sci-biology/perlprimer
Primers design for standard PCR, bisulphite PCR and Real-time PCR
sci-biology/pileup
SSAHA2-based pipeline to align reads
sci-biology/portrait
Ab initio ncRNA prediction
sci-biology/prinseq-lite
Describe, trim, reformat and convert to or form FASTA/FASTQ files
sci-biology/samstat
Statistics of BAM/SAM files