Tag: Toolkit

MoSDi 1.3 – Sequence Analysis Toolkit for Bioinformatics

MoSDi 1.3

:: DESCRIPTION

MoSDi (Motif Statistics and Discovery) contains a lot of sequence analysis algorithms, including methods for

  • motif statistics, e.g. compute the exact occurrence count distribution of a motif,
  • exact motif discovery: extraction of motifs with provably optimal p-value,
  • analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text,
  • statistics of fragment masses resulting from proteolytic cleavage of proteins,
  • computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent),
  • analysing sensitivity of spaced alignment seeds.

::DEVELOPER

Tobias Marschall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java 

:: DOWNLOAD

 MoSDi

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1737-50.
Probabilistic arithmetic automata and their applications.
Marschall T, Herms I, Kaltenbach HM, Rahmann S.

seqtk 1.3 – Toolkit for processing Sequences in FASTA/Q formats

seqtk 1.3

:: DESCRIPTION

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ MacOsX/ Linux
  • C Compiler

:: DOWNLOAD

 seqtk

:: MORE INFORMATION

TRTools v4.0.0 – Toolkit for Genome-wide analysis of Tandem Repeats

TRTools v4.0.0

:: DESCRIPTION

TRTools contains a variety of utilities for working with TR genotype files generated by HipSTR, GangSTR, and other repeat genotypers.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TRTools

:: MORE INFORMATION

Citation

Mousavi N, Margoliash J, Pusarla N, Saini S, Yanicky R, Gymrek M.
TRTools: a toolkit for genome-wide analysis of tandem repeats.
Bioinformatics. 2021 May 5;37(5):731-733. doi: 10.1093/bioinformatics/btaa736. PMID: 32805020; PMCID: PMC8097685.

OpenCRAVAT 2.2.7 – Open Custom Ranked Analysis of Variants Toolkit

OpenCRAVAT 2.2.7

:: DESCRIPTION

OpenCRAVAT is a new open source, scalable decision support system to support variant and gene prioritization. It offers a dynamic GUI, allowing users to easily, download tools from an extensive resource catalog, create customized pipelines, run jobs at speeds that exceed current variant annotation API services, and explore results in a richly detailed viewing environment.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

OpenCRAVAT

:: MORE INFORMATION

Citation

Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R.
Integrated Informatics Analysis of Cancer-Related Variants.
JCO Clin Cancer Inform. 2020 Mar;4:310-317. doi: 10.1200/CCI.19.00132. PMID: 32228266; PMCID: PMC7113103.

CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.
Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

GROK 1.1.1 – Genomic Region Operation Toolkit

GROK 1.1.1

:: DESCRIPTION

GROK is “Swiss Army knife” library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

 GROK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):200-6. doi: 10.1109/TCBB.2012.170.
Genomic region operation kit for flexible processing of deep sequencing data.
Ovaska K1, Lyly L, Sahu B, J?nne OA, Hautaniemi S.

PAGIT 1.01 – Post Assembly Genome Improvement Toolkit

PAGIT 1.01

:: DESCRIPTION

PAGIT (Post Assembly Genome Improvement Toolkit) is a tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation.

::DEVELOPER

PAGIT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PAGIT

:: MORE INFORMATION

Citation

Nat Protoc. 2012 Jun 7;7(7):1260-84. doi: 10.1038/nprot.2012.068.
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.
Swain MT1, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.

AssemblX – Toolkit for Rapid and Reliable Multi-Gene Assemblies

AssemblX

:: DESCRIPTION

AssemblX toolkit allows the assembly of up to 25 transcriptional units, consisting of many more individual DNA fragments, on a single plasmid in the host Saccharomyces cerevisiae.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res, 45 (10), e80 2017 Jun 2
AssemblX: A User-Friendly Toolkit for Rapid and Reliable Multi-Gene Assemblies
Lena Hochrein , Fabian Machens , Juergen Gremmels , Karina Schulz , Katrin Messerschmidt , Bernd Mueller-Roebe

hapsembler 2.21 – Haplotype-specific Genome Assembly Toolkit

hapsembler 2.21

:: DESCRIPTION

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  hapsembler

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

MAVisto 2.7.0 – Motif Analysis and VISualisation TOolkit

MAVisto 2.7.0

:: DESCRIPTION

MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 MAVisto

:: MORE INFORMATION

Citation

Schreiber, F. and Schwöbbermeyer H.
MAVisto: a tool for the exploration of network motifs.
Bioinformatics, 21, 3572-3574, 2005.