Mosdepth v0.2.6 – Fast BAM/CRAM Depth Calculation for WGS, Exome, or Targeted Sequencing

Mosdepth v0.2.6

:: DESCRIPTION

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Mosdepth

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.
Mosdepth: quick coverage calculation for genomes and exomes.
Pedersen BS, Quinlan AR.

BALSA 2.0 – GPU Accelerated Integrated WGS and WES Secondary Analysis

BALSA 2.0

:: DESCRIPTION

BALSA is an integrated solution for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis.

::DEVELOPER

L3 Bioinformatics Limited

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GPU

:: DOWNLOAD

 BALSA

:: MORE INFORMATION

Citation

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.
Luo R, Wong YL, Law WC, Lee LK, Cheung J, Liu CM, Lam TW.
PeerJ. 2014 Jun 3;2:e421. doi: 10.7717/peerj.421.

Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads

Phusion 2.1c

:: DESCRIPTION

Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.

::DEVELOPER

Zemin Ning ( zn1@sanger.ac.uk ),Yong Gu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Phusion

:: MORE INFORMATION

Citation

The phusion assembler.
Mullikin JC and Ning Z
Genome research2003;13;1;81-90

cnvHiTSeq 0.1.2 – Detect and Genotype CNVs in WGS data

cnvHiTSeq 0.1.2

:: DESCRIPTION

cnvHiTSeq is a  software for detecting and genotyping CNVs in WGS data

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 cnvHiTSeq

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R120. doi: 10.1186/gb-2012-13-12-r120.
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.
Bellos E, Johnson MR, M Coin LJ.

RePS 2.0 – WGS Sequence Assembler

RePS 2.0

:: DESCRIPTION

RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering

::DEVELOPER

BGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RePS

:: MORE INFORMATION

Citation:

Wang J, Wong GK, Ni P, etal.
RePS: a sequence assembler that masks exact repeats identified from the shotgun data.
Genome Res 2002; 12: 824-31.

HnaTyping 20130706 – HNA Genotyping From WGS

HnaTyping 20130706

:: DESCRIPTION

HnaTyping is a software for genotyping of human neutrophil antigens (HNA) from whole genome sequencing data

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

HnaTyping

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HnaTyping

:: MORE INFORMATION

Citation

BMC Med Genomics. 2013 Sep 12;6:31. doi: 10.1186/1755-8794-6-31.
Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.
Chu HT1, Lin H, Tsao TT, Chang CF, Hsiao WW, Yeh TJ, Chang CM, Liu YW, Wang TY, Yang KC, Chen TJ, Chen JC, Chen KC, Kao CY.

Fermi 1.1 – WGS de novo Assembler based on the FMD-index for large Genomes

Fermi 1.1

:: DESCRIPTION

Fermi is a de novo assembler for Illumina reads from whole-genome short-gun sequencing. It also provides tools for error correction, sequence-to-read alignment and comparison between read sets. It uses the FMD-index, a novel compressed data structure, as the key data representation.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Fermi

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 15;28(14):1838-44. doi: 10.1093/bioinformatics/bts280. Epub 2012 May 7.
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.
Li H.

Quake 0.3.5 – Detect & Correct Substitution Sequencing Errors in WGS Data Sets

Quake 0.3.5

:: DESCRIPTION

Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections,  which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Quake

:: MORE INFORMATION

Citation

Genome Biology 2010, 11:R116
Quake: quality-aware detection and correction of sequencing errors
David R Kelley, Michael C Schatz and Steven L Salzberg