BOL: Related items

iSeqQC: a tool for expression-based quality control in RNA sequencing

BioStar — Sun, 16 Feb 2020 08:47:17 -0600

iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Jit — Thu, 11 Feb 2021 21:39:05 -0600

Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

cisMuton: caller that detects SNVs/indels by comparing target (foreground) and control (background) samples

Jit — Tue, 11 Feb 2020 05:55:00 -0600

cisMuton is a caller that detects SNVs/indels by comparing target (foreground) and control (background) samples.

cisMuton calls mutations from target capture regions, which are defined by the overlapping regions of ${GROUP}.target.bed and ${GROUP}.gene.bed.

Please read the Quick Start Guide for cisCall first for an outline of how to run cisMuton.

Address of the bookmark: https://static.ciscall.org/cisCall5_doc/index.html

pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

Jit — Thu, 24 May 2018 10:06:52 -0500

pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.

Address of the bookmark: https://github.com/PacificBiosciences/pbalign

tinycov: standalone command line utility written in python to plot coverage from a BAM file

Jit — Mon, 23 Mar 2020 06:22:08 -0500

Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter.

To install the stable version: pip3 install --user tinycov

To install the development version:

git clone https://github.com/cmdoret/tinycov.git
cd tinycov
pip install .

Address of the bookmark: https://github.com/cmdoret/tinycov

sam to bam conversion !!

Jit — Fri, 26 Jan 2018 02:36:18 -0600

To do sam to bam conversion, follow the following commands :-

Code:

$ samtools view -b -S file.sam > file.bam

Then you will need to use

Code:

$ samtools sort file.bam file-sorted

followed by

Code:

$ samtools index  file-sorted.bam

in order to get an indexed file.

If you just type

Code:

$ samtools

or samtools followed by the name of one of the samtools commands, you will get a few lines of help giving the correct syntax for that command,

CNIDARIA: fast, reference-free phylogenomic clustering

Shruti Paniwala — Thu, 16 Jun 2016 17:55:17 -0500

Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

Jit — Tue, 12 Dec 2017 17:23:31 -0600

MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

Address of the bookmark: https://github.com/marbl/MashMap

FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)

Jit — Fri, 13 Jul 2018 17:27:01 -0500

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Its underlying procedure follows a similar workflow as described by Goris et al. 2007. However, it avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity estimates. Based on our experiments with complete and draft genomes, its accuracy is on par with BLAST-based ANI solver and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More details about its speed, accuracy and potential applications are described here: "High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries".

Address of the bookmark: https://github.com/ParBLiSS/FastANI