:: DESCRIPTION
ngs-bits is a collection of tools for short-read data analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schroeder CM, Hilke FJ, Löffler MW, Bitzer M, Lenz F, Sturm M.
A comprehensive quality control workflow for paired tumor-normal NGS experiments.
Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032. PMID: 28130233.
:: DESCRIPTION
LoQuM assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Accurate estimation of short read mapping quality for next-generation genome sequencing.
Ruffalo M, Koyutürk M, Ray S, LaFramboise T.
Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.
:: DESCRIPTION
ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.
::DEVELOPER
the Computational Biology Group (CBG)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinformatics, vol. 12 p. 119
:: DESCRIPTION
BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Sep 18;43(16):e107. doi: 10.1093/nar/gkv533.
BatAlign: an incremental method for accurate alignment of sequencing reads.
Lim JQ, Tennakoon C, Guan P, Sung WK.
:: DESCRIPTION
SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.
:: DESCRIPTION
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter.
:DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2009;10(9):R98. Epub 2009 Sep 17.
Simultaneous alignment of short reads against multiple genomes.
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.
:: DESCRIPTION
MICA-aligner is a new short-read aligner that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2015 Apr 23;16 Suppl 7:S10. doi: 10.1186/1471-2105-16-S7-S10. Epub 2015 Apr 23.
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).
Luo R, Cheung J, Wu E, Wang H, Chan SH, Law WC, He G, Yu C, Liu CM, Zhou D, Li Y, Li R, Wang J, Zhu X, Peng S, Lam TW.
:: DESCRIPTION
ngsShoRT algorithms are designed to pre-process Single Read (SR) or Paired-end (PE)/Mate-pair (MP) reads in FastQ format or Illumina’s native QSEQ format (with compressed file support). It privides parallel processing by multi-threading to deal with large volume of data and reduce running time. Another unique feature of ngsShoRT is that it was designed to handle PE/MP reads generically using paired-end specific modules.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Software for pre-processing Illumina next-generation sequencing short read sequences.
Chen C, Khaleel SS, Huang H, Wu CH.
Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8
:: DESCRIPTION
Kpath (PathEnc) is a reference-based compression software of short read data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Reference-based compression of short-read sequences using path encoding.
Kingsford C, Patro R.
Bioinformatics. 2015 Feb 2. pii: btv071.
:: DESCRIPTION
GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps.
GapMis is a tool for pairwise sequence alignment with a single gap.
GapMis-OMP is the OpenMP-based version of GapMis.
libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
GapsMis , GapMis , GapMis-OMP , libgapmis
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.
libgapmis: extending short-read alignments.
Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.
GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.
Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.
Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler.
Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library
