BOL: Related items

Sample bandage input file for visual analysis

Jit — Wed, 06 Jan 2021 03:51:50 -0600

Sample bandage input file for visual analysis ...

Software for genome assembly !

LEGE — Sun, 30 Aug 2020 09:51:38 -0500

List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

IVA: accurate de novo assembly of RNA virus genomes

Neel — Wed, 23 Jun 2021 07:51:59 -0500

IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

https://pubmed.ncbi.nlm.nih.gov/25725497/

Address of the bookmark: https://github.com/sanger-pathogens/iva

RagTag: a collection of software tools for scaffolding and improving modern genome assemblies

Jit — Sat, 11 Sep 2021 00:28:14 -0500

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Homology-based misassembly correction
Homology-based assembly scaffolding and patching
Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

Illumina based assembly pipeline steps !

Surabhi Chaudhary — Fri, 10 Dec 2021 06:22:54 -0600

Illumina

Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter trimming (fastp)
Removal of host reads (Kraken 2; optional)
Variant calling
1. Read alignment (Bowtie 2)
2. Sort and index alignments (SAMtools)
3. Primer sequence removal (iVar; amplicon data only)
4. Duplicate read marking (picard; optional)
5. Alignment-level QC (picard, SAMtools)
6. Genome-wide and amplicon coverage QC plots (mosdepth)
7. Choice of multiple variant calling and consensus sequence generation routes (iVar variants and consensus; default for amplicon data || BCFTools, BEDTools; default for metagenomics data)
  - Variant annotation (SnpEff, SnpSift)
  - Consensus assessment report (QUAST)
  - Lineage analysis (Pangolin)
  - Clade assignment, mutation calling and sequence quality checks (Nextclade)
  - Individual variant screenshots with annotation tracks (ASCIIGenome)
8. Intersect variants across callers (BCFTools)
De novo assembly
1. Primer trimming (Cutadapt; amplicon data only)
2. Choice of multiple assembly tools (SPAdes || Unicycler || minia)
  - Blast to reference genome (blastn)
  - Contiguate assembly (ABACAS)
  - Assembly report (PlasmidID)
  - Assembly assessment report (QUAST)
Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)

CrossMap: program for genome coordinates conversion between different assemblies

Rahul Nayak — Tue, 25 Jan 2022 17:59:32 -0600

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

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

Comparative genomics visualisation tools !

Neel — Thu, 17 Feb 2022 05:37:55 -0600

Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

The complete sequence of a human genome

Neel — Thu, 31 Mar 2022 23:58:18 -0500

The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

JBrowse 2: a modular genome browser with views of synteny and structural variation

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile