BCALM 2.2.1 – de Bruijn Graph Compacation from Reads

BCALM 2.2.1

:: DESCRIPTION

BCALM is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BCALM

:: MORE INFORMATION

Citation:

Rayan Chikhi, Antoine Limasset and Paul Medvedev,
Compacting de Bruijn graphs from sequencing data quickly and in low memory,
Bioinformatics, 32 (12), i201-i208 2016 Jun 15

IsoCon 0.3.2 – Deriving Finished Transcript Sequences from Iso-Seq reads

IsoCon 0.3.2

:: DESCRIPTION

IsoCon is a tool for reconstructing highly similar sequences present in a dataset of from long noisy reads

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

IsoCon

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D. Makova, Paul Medvedev
Deciphering highly similar multigene family transcripts from iso-seq data with isocon.
Nature Communications, 9(1):4601, 2018

scarpa 0.241 – Scaffolding Reads with Practical Algorithms

scarpa 0.241

:: DESCRIPTION

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 scarpa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):428-34. doi: 10.1093/bioinformatics/bts716. Epub 2012 Dec 29.
SCARPA: scaffolding reads with practical algorithms.
Donmez N, Brudno M.

CORA 1.1.5b – compressive-acceleration tool for NGS Read Mapping methods

CORA 1.1.5b

:: DESCRIPTION

CORA is a compressive-acceleration tool for NGS read mapping methods. When plugged into existing mapping tools, CORA achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CORA

:: MORE INFORMATION

Citation:

Deniz Yorukoglu, Y. William Yu, Jian Peng, Bonnie Berger.
Compressive Mapping for Next-generation Sequencing
Nature Biotechnology 34, 374-376 (2016) doi:10.1038/nbt.3511.

ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

  BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.

bcm-ace-plots – Reads in an Ace format Assembly File produced by the Phrap

bcm-ace-plots

:: DESCRIPTION

bcm-ace-plots reads in an Ace format assembly file produced by the Phrap (Green et al.) assembly software. Using special tags in the read names, bcm-ace-plots will plot the template coverage, the template span, the coverage, the BAC coverage, the WGS coverage, quality, and high quality discrepancies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java

:: DOWNLOAD

bcm-ace-plots

:: MORE INFORMATION

NanoOK 1.33 – Alignment and Analysis of Nanopore Reads

NanoOK 1.33

:: DESCRIPTION

NanoOK is a tool from TGAC for alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox
  • Java

:: DOWNLOAD

  NanoOK

:: MORE INFORMATION

Citation:

NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP.
Bioinformatics. 2015 Sep 17. pii: btv540

PaPaRa 2.5 – PArsimony-based Phylogeny-Aware Read alignment program

PaPaRa 2.5

:: DESCRIPTION

PaPaRa is a PArsimony-based Phylogeny-Aware Read alignment program

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • C Compier

:: DOWNLOAD

 PaPaRa

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Aug 9;13:196. doi: 10.1186/1471-2105-13-196.
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
Alachiotis N, Berger SA, Stamatakis A.

Trimmomatic 0.39 – A Flexible Read Trimming tool for Illumina NGS data

Trimmomatic 0.39

:: DESCRIPTION

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  Trimmomatic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 28.
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM1, Lohse M, Usadel B.