EMBL2checklists 0.6 – Converts EMBL-formatted flatfiles to ENA Checklists

EMBL2checklists 0.6

:: DESCRIPTION

EMBL2checklists converts EMBL- or GenBank-formatted flat files to submission-ready checklists (i.e., tab-separated spreadsheets) for submission to ENA via the interactive Webin submission system.

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Python

:: DOWNLOAD

EMBL2checklists

:: MORE INFORMATION

Citation

Gruenstaeudl M, Hartmaring Y.
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA.
PLoS One. 2019 Jan 10;14(1):e0210347. doi: 10.1371/journal.pone.0210347. PMID: 30629718; PMCID: PMC6328100.

annonex2embl 1.0.3 – Preparation of Annotated DNA Sequences for Bulk Submissions to ENA

annonex2embl 1.0.3

:: DESCRIPTION

annonex2embl Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA via the Webin-CLI submission tool

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Python

:: DOWNLOAD

 annonex2embl 

:: MORE INFORMATION

Citation

Gruenstaeudl M.
annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA.
Bioinformatics. 2020 Jun 1;36(12):3841-3848. doi: 10.1093/bioinformatics/btaa209. PMID: 32227202.

SPNConverter 1.0 – Tool to Convert Graphs into GraphML Format

SPNConverter 1.0

:: DESCRIPTION

SPNConverter enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML) to Graphml format.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • CytoScape
:: DOWNLOAD

 SPNConverter

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Oct 1;29(19):2507-8. doi: 10.1093/bioinformatics/btt421. Epub 2013 Aug 1.
SPNConverter: a new link between static and dynamic complex network analysis.
Dent JE1, Yang X, Nardini C.

DNAcompact 20130829 – Genome Compression algorithm with/without Reference

DNAcompact 20130829

:: DESCRIPTION

DNA-COMPACT is a software of DNA COMpression based on a pattern-aware contextual modeling technique.

::DEVELOPER

DNAcompact team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 DNAcompact

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.
Li P1, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X.

FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat – Conversion between Tab-delimited files and FASTA/ FastQ Format

FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: DESCRIPTION

FastaFormat: Convert tab-delimited files into fasta format. Includes a quality score safe option (-q) for converting quality score files.

FastQFormat: Convert tab-delimited sequence and quality score files into fastQ format.

UnFastaFormat: Convert fasta files into tab-delimited format. Includes a quality score safe option (-q) for converting quality score files.

UnFastQFormat: Convert fastq files into tab-delimited format. Outputs sequences and quality scores into separate files. Edits sequence titles. Support for NCBI and Illumina formats.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Perl

:: DOWNLOAD

 FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: MORE INFORMATION

TableParser – Extract Sequences from Tab-delimited Assembly Alignment Files

TableParser

:: DESCRIPTION

TableParser: Simple tool for extracting sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parses out contigs, singletons, and assembled reads into separate files.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 TableParser

:: MORE INFORMATION

AceParser 1.33 – Parse an Ace file (Phred/Phrap output) into a tab-delimited Assembly Alignment file

AceParser 1.33

:: DESCRIPTION

AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AceParser

:: MORE INFORMATION

SnoWhite 2.0.3 – An Aggressive Cleaning Pipeline for DNA Sequence Reads

SnoWhite 2.0.3

:: DESCRIPTION

Snowhite is a pipeline designed to flexibly and aggressively clean sequence reads (gDNA or cDNA) prior to assembly. It takes in and returns fasta formatted sequence and (optionally) quality files.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SnoWhite

:: MORE INFORMATION

Citation

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Barker MS, Dlugosch KM, Dinh L, Challa RS, Kane NC, King MG, Rieseberg LH.
Evol Bioinform Online. 2010 Oct 20;6:143-9. doi: 10.4137/EBO.S5861.