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http://sourceforge.net/projects/seqexpress/

A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.

Proper citation: SeqExpress (RRID:SCR_004013) Copy   

•   Source: SciCrunch Registry

http://genomics.princeton.edu/AndolfattoLab/MSG.html

A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.

Proper citation: MSG (RRID:SCR_004161) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/perm/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Proper citation: PerM (RRID:SCR_004223) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hlaseq/

An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.

Proper citation: HLASeq (RRID:SCR_004185) Copy   

•   Source: SciCrunch Registry

http://pass.cribi.unipd.it/cgi-bin/pass.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.

Proper citation: PASS-bis (RRID:SCR_004176) Copy   

•   Source: SciCrunch Registry

http://www.cs.gsu.edu/~serghei/?q=drut

Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.

Proper citation: DRUT (RRID:SCR_004351) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/act/

A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Proper citation: ACT: Artemis Comparison Tool (RRID:SCR_004507) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.wayne.edu/software/squeezambler/

Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.

Proper citation: Squeezambler (RRID:SCR_004385) Copy   

•   Source: SciCrunch Registry

https://www.tgen.org/research/research-divisions/neurogenomics/supplementary-data/sniper-hd-improved-genotype-calling-accuracy.aspx#.UjmeKb5OKM8

Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.

Proper citation: SNiPer-HD (RRID:SCR_004383) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vanator-cvr/

A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.

Proper citation: Vanator (RRID:SCR_004370) Copy   

•   Source: SciCrunch Registry

http://www.csd.uwo.ca/~ilie/BOND/

Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.

Proper citation: Basic OligoNucleotide Design (RRID:SCR_004492) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/

Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html

A multiple-sample, technology-aware SNP and indel caller.

Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy   

•   Source: SciCrunch Registry

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146

An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.

Proper citation: NuChart (RRID:SCR_004703) Copy   

•   Source: SciCrunch Registry

http://matsen.fhcrc.org/pplacer/

Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

Proper citation: Pplacer (RRID:SCR_004737) Copy   

•   Source: SciCrunch Registry

http://www.megx.net/tetra/

Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.

Proper citation: TETRA (RRID:SCR_004573) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/lbl.gov/biopig/

Software providing a framework for genomic data analysis using Apache Pig and Hadoop.

Proper citation: BioPig (RRID:SCR_004636) Copy   

•   Source: SciCrunch Registry

https://github.com/lmrodriguezr/nonpareil

Estimate average coverage and create Nonpareil curves for metagenomic datasets.

Proper citation: Nonpareil (RRID:SCR_004629) Copy   

•   Source: SciCrunch Registry

http://omics.informatics.indiana.edu/AbundanceBin/

An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.

Proper citation: AbundanceBin (RRID:SCR_004648) Copy   

•   Source: SciCrunch Registry

http://wiki.solariseclipse.net/PrimerDesigner

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.

Proper citation: Primer Designer (RRID:SCR_003189) Copy   

•   Source: SciCrunch Registry