BOL: Related items

HTSlib

Jit — Wed, 15 Mar 2017 11:38:05 -0500

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
HTSlib: A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Address of the bookmark: http://www.htslib.org/

Versatile genome assembly evaluation with QUAST-LG

Jit — Fri, 21 Dec 2018 22:06:31 -0600

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
New k-mer-based completeness and correctness metrics
BUSCO added for enhanced reference-free analysis
The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

List of tools frequently used while genome assembly

BioStar — Tue, 22 Jan 2019 09:39:02 -0600

List of tools frequently used while genome assembly:

I have used the following assemblers

Spades (v. 3.10.1)
CANU (v. 1.6)
Unicycler (v. v0.4.1)
Miniasm (v. 0.2-r137-dirty)

I have used the following mappers

minimap2 (v. 2.0rc1-r232)
minimap (v. 0.2-r124-dirty)
bwa (v. 0.7.12-r1039)

I have used the following polishing tools

Racon (v. not available)
Pilon (v. 1.18)
Nanopolish (v. 0.8.3)

I have used the following tools to assess genome assembly characteristics

ANI.pl (https://github.com/chjp/ANI)
CheckM (v. 1.0.7)
Prokka (v. 1.12)
QUAST (v. 2.3)
mummer (v. not available)

If you have any ideas or superior tools we have missed please let us know in the comments.

Mapping NGS

Abhimanyu Singh — Tue, 02 May 2017 07:58:07 -0500

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...
To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.
In either way, aligning your sequence reads to the reference sequence is called mapping.

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

JCVI:Python utility libraries on genome assembly, annotation and comparative genomics

Jit — Tue, 17 Mar 2020 06:19:06 -0500

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

HASLR: a hybrid assembler which uses both second and third generation sequencing reads

BioStar — Mon, 04 May 2020 02:04:03 -0500

HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.

Jit — Mon, 26 Oct 2020 21:23:36 -0500

Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

More at https://github.com/esolares/HapSolo

Address of the bookmark: https://github.com/esolares/HapSolo

Eugene V. Koonin Lab

Tue, 09 Jan 2018 05:01:15 -0600

Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.

https://www.ncbi.nlm.nih.gov/research/groups/koonin/

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Jit — Sat, 08 May 2021 21:25:00 -0500

HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies.

Address of the bookmark: https://github.com/esolares/HapSolo

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)