Scaffold_builder v2.2 – Order Contigs generated by draft sequencing along a Reference Sequence

Scaffold_builder v2.2

:: DESCRIPTION

Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Scaffold_builder

:: MORE INFORMATION

Citation

Source Code Biol Med. 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23.
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG1, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.

RefSeq 70 – NCBI Reference Sequence Database

RefSeq 70

:: DESCRIPTION

RefSeq (the Reference Sequence) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

::DEVELOPER

NCBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

RefSeq

:: MORE INFORMATION

Citation

NCBI Reference Sequences: current status, policy, and new initiatives.
Pruitt KD, Tatusova T, Klimke W, Maglott DR
Nucleic Acids Res 2009 Jan;37(Database issue):D32-6

Readaligner 201211 – Mapping (short) DNA reads into Reference Sequences

Readaligner 201211

:: DESCRIPTION

readaligner is a tool for mapping (short) DNA reads into reference sequences.

::DEVELOPER

Succinct Data Structures (SuDS) -research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC 

:: DOWNLOAD

 Readaligner

:: MORE INFORMATION

Citation:

V. Mäkinen, N. Välimäki, A. Laaksonen and R. Katainen:
Unified View of Backward Backtracking in Short Read Mapping.
To appear in Ukkonen Festschrift 2010 (Eds. Tapio Elomaa, Pekka Orponen, Heikki Mannila), Springer-Verlag, LNCS 6060, pp. 182-195, 2010.

PyroMap – Maps Pyrosequencing Reads onto Reference Sequences

PyroMap

:: DESCRIPTION

PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.

::DEVELOPER

Stanford HIVDB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PyroMap

:: MORE INFORMATION

FACS 2.1 – Align Sequences to a Reference Sequence

FACS 2.1

:: DESCRIPTION

A novel algorithm, FACS (Fast and Accurate Classification of Sequences), is introduced that can accurately and rapidly align sequences to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS is at least three times faster and more accurate than BLAT and SSAHA2 in classifying sequences when using references larger than 50Mbp.

::DEVELOPER

Henrik Stranneheim  , Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 FACS

:: MORE INFORMATION

Citation

Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J.
Classification of DNA sequences using Bloom filters.
Bioinformatics, 2010 July 1; 26(13):1595-1600. Published online 2010 May 13. doi:10.1093/bioinformatics/btq230

Refcomp 4.x – Compare Reference Sequence with Consensus Sequence

Refcomp 4.x

:: DESCRIPTION

Refcomp was designed to analyze sequencing traces which contains data from strictly homozygous samples (eg. cloned DNA, mitochondrial DNA, etc.).  This data represents a special case which can be analyzed for mismatches with a known reference sequence.  Refcomp will determine the high quality positions within an assembled DNA contig and produce a report listing sites which differ from a defined reference sequence.

Refcomp is designed as a member of an integrated suite of sequence analysis applications which includes Phred,Phrap and Consed, and is not a stand alone program.

::DEVELOPER

Dr. Deborah Nickerson’s lab at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Solaris/SGI IRIX/Compaq Tru64 Alpha/HP-UX

:: DOWNLOAD

Refcomp

:: MORE INFORMATION

RefComp is available for free to researchers at academic and non-profit institutions. To aquire RefComp, please Read the Academic License Agreement, and fill in and submit the request form.

Citation:

Rieder et al,Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome., Nucleic Acids Research, 26: 967-973, 1998.