BOL: Related items

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments

LEGE — Mon, 22 Sep 2025 23:51:02 -0500

termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

Jit — Mon, 05 Apr 2021 11:19:43 -0500

With kallisto | bustools you can

Generate a cell x gene or cell x transcript equivalence class count matrix
Perform RNA velocity and single-nuclei RNA-seq analsis
Quantify data from numerous technologies such as 10x, inDrops, and Dropseq.
Customize workflows for new technologies and protocols.
Process feature barcoding data such as CITE-seq, REAP-seq, MULTI-seq, Clicktags, and Perturb-seq.
Obtain QC reports from single-cell RNA-seq data

The kallisto | bustools workflow is described in:

Páll Melsted*, A. Sina Booeshaghi*, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi (Joseph) Min, Eduardo da Veiga Beltrame, Kristján Eldjárn Hjörleifsson, Jase Gehring & Lior Pachter† Modular and efficient pre-processing of single-cell RNA-seq, Nature Biotechnology (2021).

Documentation and tutorials for the kallisto bustools workflow are available at http://pachterlab.github.io/kallistobustools.

https://www.nature.com/articles/s41587-021-00870-2

Address of the bookmark: https://pachterlab.github.io/kallistobustools/

Reference-free prediction of rearrangement breakpoint reads

Neel — Thu, 08 Mar 2018 05:05:25 -0600

lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Jit — Tue, 12 Jun 2018 12:41:10 -0500

Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs).

Address of the bookmark: https://github.com/ruping/Breakpointer

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

Rahul Nayak — Thu, 14 May 2020 15:09:52 -0500

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

BioStar — Fri, 21 Sep 2018 10:19:52 -0500

Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore

Neel — Fri, 19 Oct 2018 08:48:43 -0500

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy.

Address of the bookmark: https://github.com/ruanjue/wtdbg2

Genome assembly tutorial "Genome Assembly for short and long reads"

Jit — Sat, 19 Jan 2019 17:29:53 -0600

In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

How to perform basic quality checks on the input data
How to run a short read assembler on Illumina data
How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
How to improve the accuracy of a long read assembly using short reads
How to assess the quality of an assembly

https://bioinformaticsdotca.github.io/high-throughput_biology_2017

Address of the bookmark: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab