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sci-biology/NGSEPcore-bin
NGSEP (CNV and indel discovery)
sci-biology/Rcorrector
Error correction for Illumina RNA-seq reads
sci-biology/angsd
Population genetics analysis package
sci-biology/epga
De novo assembler using distribution of reads and insert size
sci-biology/exonerate-gff3
exonerate-2.2.0 with patches to add GFF3 formatted output
sci-biology/freebayes
Bayesian gen. variant detector to find short polymorphisms
sci-biology/grabix
Provide random access to text files BGZF compressed with bgzip
sci-biology/lighter
NGS reads corrector
sci-biology/lumpy-sv
Probabilistic framework for structural variant discovery
sci-biology/megahit
Metagenome assembler using succinct de Bruijn graph approach with CUDA
sci-biology/nanopolish
Signal-level analysis of Oxford Nanopore sequencing data
sci-biology/nxtrim
Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
sci-biology/pbbam
PacBio modified BAM file format
sci-biology/perga
Paired End Reads Guided Assembler
sci-biology/sabre
Barcode demultiplexing and trimming tool for Illumina FastQ files
sci-biology/samstat
Statistics of BAM/SAM files
sci-biology/scythe
Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa
sci-biology/snpomatic
Stringent short-read aligner supporting filters and various output formats
sci-biology/sga
String Graph OLC Assembler for short reads (overlap-layout-consensus)
sci-biology/vcflib
VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)
sci-biology/vt
A tool set for short variant discovery in genetic sequence data
sci-biology/Fastaq
Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers
sci-biology/bx-python
Library for rapid implementation of genome scale analyses
sci-biology/deeptools
Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig
sci-biology/dcmstack
DICOM to Nifti coversion
sci-biology/dipy
Computational neuroanatomy project focusing on diffusion MRI
sci-biology/gffutils
GFF and GTF file manipulation and interconversion
sci-biology/nilearn
Fast and easy statistical learning on NeuroImaging data
sci-biology/nitime
Time-series analysis of neuroscience data
sci-biology/samri
Small Animal Magnetic Resonance Imaging
sci-biology/ants
Advanced Normalitazion Tools for neuroimaging
sci-biology/assembly-stats
Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)
sci-biology/bam-readcount
Count DNA sequence reads in BAM files and other statistics calculations
sci-biology/flexbar
Barcode, MID tag and adapter sequence removal
sci-biology/diamond
Alternative of blastp/blastx searches using DNA short reads through protein db
sci-biology/genepop
Population genetics analysis
sci-biology/jellyfish
k-mer counter within reads for assemblies
sci-biology/lastz
A pairwise DNA sequence aligner, a BLASTZ replacement
sci-biology/nextclip
Split Illumina Nextera long mate-pairs
sci-biology/proda
Multiple alignment of protein sequences with repeated and shuffled elements
sci-biology/stacks
Analyze restriction enzyme data, draw gen. maps, population genomics
sci-biology/yaha
DNA mapper for single-end reads to detect structural variants (SV)
sci-chemistry/concoord
Protein conformations around a known structure based on geometric restrictions
sci-chemistry/pales-bin
Prediction of alignment from structure
sci-chemistry/ssp
Secondary structure propensities
sci-chemistry/MotionCor2
Correction of electron beam-induced sample motion
sci-chemistry/drawxtl
Crystal structure drawings from structural data
sci-chemistry/gnome-chemistry-utils
Programs and library containing GTK widgets and C++ classes related to chemistry
sci-chemistry/nmrpipe
Spectral visualisation, analysis and Fourier processing
sci-chemistry/mics
Prediction of Protein Structural Motifs from NMR Chemical Shifts