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sci-biology/biobambam2

Tools for bam file processing (libmaus2)

sci-biology/BRAKER

Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS

sci-biology/KING

Check family relationship and infer population structure

sci-biology/GAL

Genome Annotation Library (incl. fasta_tool)

sci-biology/KaKs_Calculator

Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates

sci-biology/SEECER

SEquence Error Corrector for RNA-Seq reads

sci-biology/abacas

Order and orientate DNA contigs even via 6-frame protein alignments

sci-biology/afni

Advanced Normalitazion Tools for neuroimaging

sci-biology/align_to_scf

View trace information at a given position missing from Roche .ace files

sci-biology/bamql

Extract reads from BAM files

sci-biology/bambus

Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle

sci-biology/barrnap

Predict Bacterial and Archaeal rRNA genes and output in GFF3 format

sci-biology/bedops

Manipulate BED file (alternative to bedtools)

sci-biology/codonw

Multivariate statistical analysis of codon and amino acid usage

sci-biology/coral

Error corrector for Illumina and Roche/454 reads using multiple alignment info

sci-biology/fsa

Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot

sci-biology/germline

Find shared segments of Identity by Descent (IBD) between pairs of individuals

sci-biology/glean

Merge various gene prediction into one (unsupervised learning system)

sci-biology/graf-bin

Find closely related subjects using SNP genotype data, validate pedigree file

sci-biology/mrfast

Micro Read Fast Alignment Search Tool

sci-biology/nrcl

Containment clustering and layout utility for processing pairwise alignments

sci-biology/ntCard

Estimate k-mer coverage histogram of genomics data

sci-biology/scan_for_matches

Pattern search through DNA sequences (aka patscan)

sci-biology/sickle

Windowed adaptive quality-based trimming tool for FASTQ data

sci-biology/snap

HMM-based prokaryotic and eukaryotic gene prediction tool

sci-biology/swissknife

Perl library of modules to manipulate SwissProt flatfiles

sci-biology/tigr-foundation-libs

TIGR Foundation for C++

sci-biology/trf-bin

Tandem Repeats Finder

sci-biology/trinityrnaseq

Transcriptome assembler for RNA-seq reads

sci-biology/twinscan

iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline

sci-biology/BBmap

Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool

sci-biology/MeV

Multiple experiment Viewer for genomic data analysis

sci-biology/VarScan

Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)

sci-biology/SnpEff

SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF

sci-biology/VarScan-bin

Variant detection (germline, multi-sample, somatic mut., CNA), SNP

sci-biology/act-bin

DNA contig sequence comparison tool supplementing Artemis

sci-biology/beagle

Genotype calling/phasing, imputation of ungenotyped markers

sci-biology/fastqc

Quality control FASTA/FASTQ sequence files

sci-biology/genomeview-bin

Genome browser and annotation tool

sci-biology/jannovar-bin

Exome annotation tool (upstream jar binaries)

sci-biology/imagej

Image Processing and Analysis in Java

sci-biology/jtreeview-bin

Viewer for Microarray Data in PCL or CDT formats

sci-biology/vague-bin

GUI for Velvet de novo assembler

sci-biology/trimmomatic

Illumina adapter trimming tool

sci-biology/hisat2

Align DNA reads to a population of genomes

sci-biology/RAILS

Cobbler and RAILS scaffolding tools acting on SAM streams

sci-biology/SPAdes

De novo de Bruijn genome assembler overcoming uneven coverage

sci-biology/AlignGraph

Reference-genome-assisted asssembly of contigs/scaffolds using PE reads

sci-biology/NGSEPcore

NGSEP (CNV and indel discovery)

sci-biology/BRANCH

Extend partial transcripts with sequence from other reads or genomic contigs