CoLoRMap – Correcting Long noisy Reads by Mapping short reads

CoLoRMap

:: DESCRIPTION

CoLoRMap is a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CoLoRMap

:: MORE INFORMATION

Citation

Haghshenas E, Hach F, Sahinalp SC, Chauve C.
CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463. PMID: 27587673.

MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.

SlideSort v2 – All Pairs Similarity Search for Short Reads

SlideSort v2

:: DESCRIPTION

SlideSort is fast and exact method that can find all similar pairs from a string pool in terms of edit distance.

::DEVELOPER

Kana Shimizu

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

SlideSort

:: MORE INFORMATION

Citation

Kana Shimizu and Koji Tsuda
“SlideSort:All pairs similarity search for short reads“,
Bioinformatics (2011) 27 (4): 464-470

Novoalign 4.03.03 – Aligner Capable of Gapped Alignment for Illumina Short Reads

Novoalign 4.03.03

:: DESCRIPTION

Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

::DEVELOPER

Novocraft Technologies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX

:: DOWNLOAD

Novoalign

:: MORE INFORMATION

SlideSort-BPR 1.0.0 – Finding Differences between Multiple Short-read datasets without Reference Genome

SlideSort-BPR 1.0.0

:: DESCRIPTION

SlideSort-BPR is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads

:: DEVELOPER

SlideSort-BPR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SlideSort-BPR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 29. pii: btu360. [Epub ahead of print]
Reference-free Prediction of Rearrangement Breakpoint Reads.
Wijaya E1, Shimizu K2, Asai K3, Hamada M

BS Seeker 2.1.8 – Mapping of Bisulfite-treated Short Reads

BS Seeker 2.1.8

:: DESCRIPTION

BS Seeker (Bisulfite sequencing) performs accurate and fast mapping of bisulfite-treated short reads. It aligns Bisulfite-treated reads generated from the Cokus et al’s library protocol (with tags) or the Lister et al’s library protocol (with no tags).

::DEVELOPER

Matteo Pellegrini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Bowtie
Python

:: DOWNLOAD

BS Seeker

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Nov 10;14:774. doi: 10.1186/1471-2164-14-774.
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY1, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203.
BS Seeker: precise mapping for bisulfite sequencing.
Chen PY, Cokus SJ, Pellegrini M.

BitMapper 2.0.0.7 – Short Reads Alignment Tool

BitMapper 2.0.0.7

:: DESCRIPTION

BitMapper is an efficient reads mappers for short reads of equal length. It is designed to output all mapping locations for each reads.

::DEVELOPER

BitMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BitMapper

:: MORE INFORMATION

Citation

BitMapper: an efficient all-mapper based on bit-vector computing.
Cheng H, Jiang H, Yang J, Xu Y, Shang Y.
BMC Bioinformatics. 2015 Jun 11;16(1):192. doi: 10.1186/s12859-015-0626-9.

MaSuRCA 4.0.4 – Whole Genome Short Read Assembler

MaSuRCA 4.0.4

:: DESCRIPTION

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MaSuRCA

:: MORE INFORMATION

Citation

The MaSuRCA genome assembler.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.
Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476.

Minia 3.2.6 – Short-read Assembler based on a de Bruijn graph

Minia 3.2.6

:: DESCRIPTION

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day

::DEVELOPER

Rayan Chikhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Minia

:: MORE INFORMATION

Citation

R. Chikhi, G. Rizk.
Space-efficient and exact de Bruijn graph representation based on a Bloom filter,
WABI 2012

CUSHAW3 3.0.3 – Sensitive and Accurate Gapped Short-read Alignment

CUSHAW3 3.0.3

:: DESCRIPTION

CUSHAW3 (the third distribution of CUSHAW software package for next-generation sequencing read alignment) is an open-source parallelized, sensitive and accurate short-read aligner.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

CUSHAW3

:: MORE INFORMATION

Citation:

Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.
González-Domínguez J, Liu Y, Schmidt B.
PLoS One. 2016 Jan 5;11(1):e0145490. doi: 10.1371/journal.pone.0145490.

PLoS One. 2014 Jan 22;9(1):e86869. doi: 10.1371/journal.pone.0086869. eCollection 2014.
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Liu Y1, Popp B2, Schmidt B1.