BOL: Related items

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

Genobuntu: Package for Next Generation Sequencing and Genome Assembly

BioStar — Mon, 18 May 2020 16:47:56 -0500

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

Velvet
MiB
SSAKE
EULER
VCAKE
ABySS
ALLPATHS
Celera
SHARCGS
Allpaths
IDBA
TAIPAN
Edena
SOAPdenovo
Maq
IDBA-UD
No. of Reads present in the Ref. Seq.
ART NGS Reads Simulator
HiTEC, FASTQC
Minimum Description Length
SOAPaligner
Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

Address of the bookmark: https://github.com/lh3/bfc

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

FiNGS: Filters for Next Generation Sequencing

Neel — Sat, 27 Feb 2021 01:18:35 -0600

Key features

Filters SNVs from any variant caller to remove false positives
Calculates metrics based on BAM files and provides filtering not possible with other tools
Fully user-configurable filtering (including which filters to use and their thresholds)
Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules

Rahul Nayak — Thu, 04 Oct 2018 16:30:44 -0500

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

Address of the bookmark: https://github.com/broadinstitute/VariantBam