BOL: Related items

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Mon, 17 Aug 2020 05:25:10 -0500

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

sunbeam: A robust, extensible metagenomics pipeline

Jit — Thu, 18 Jun 2020 06:58:52 -0500

Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin privileges, and can be deployed on most Linux workstations and clusters. To read more, check out our paper in Microbiome.

https://sunbeam.readthedocs.io/en/latest/

Address of the bookmark: https://github.com/sunbeam-labs/sunbeam

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads

Rahul Nayak — Sun, 14 Mar 2021 09:42:47 -0500

AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Abhi — Tue, 05 Sep 2023 07:31:35 -0500

MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

QuasR: Quantification and annotation of short reads in R

Neel — Fri, 13 Aug 2021 07:44:05 -0500

The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and HISAT2, through the Rhisat2 package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html

Circlator: automated circularization of genome assemblies using long sequencing reads

Poonam Mahapatra — Tue, 15 May 2018 09:42:32 -0500

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.

Address of the bookmark: http://sanger-pathogens.github.io/circlator/

iMAGine - in silico MetAGenomics pipeline

BioStar — Sat, 06 Jul 2024 04:32:18 -0500

iMAGine is a metagenomic workflow which includes filtering, assembling, and binning.

This workflow includes the following tools which are needed to be installed in the system.

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.

Jit — Fri, 14 Feb 2020 14:23:30 -0600

This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.

Here is an illustration of this pipeline:

Address of the bookmark: https://github.com/BGI-Qingdao/SLR-superscaffolder

CoLoRMap: Correcting Long Reads by Mapping short reads

Jit — Mon, 20 Aug 2018 14:17:05 -0500

Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, 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. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Address of the bookmark: https://github.com/sfu-compbio/colormap

dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation

Jit — Mon, 29 May 2017 05:39:29 -0500

dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE. Similar resources on the web include CAZy database and CAT. All data in dbCAN are generated based on the family classification from CAZy database while it has the following unique features compared with CAZy database and CAT:

dbCAN provides the capability of automated and comprehensive CAZyme annotation of a given genome submitted by the user;
dbCAN provides an explicitly defined signature domain for each and every CAZyme family along with its location in all the relevant full-length CAZyme proteins in all sequenced genomes;
dbCAN provides the most complete set of metagenomic CAZyme genes published so far and represents the first step towards discovering novel CAZyme catalysts in metagenomes;
dbCAN provides a subfamily classification of the existing CAZyme families based on sequence similarities;
dbCAN make all pre-computed data freely available to the public, including sequence alignments, hidden markov models (HMMs) and phylogenies of the signature domain regions in each and every CAZyme family and subfamily.

dbCAN is updated regularly when CAZy database created new families based on latest literature.

Address of the bookmark: http://csbl.bmb.uga.edu/dbCAN/index.php