1. How to perform basic quality checks on the input data
2. How to run a short read assembler on Illumina data
3. How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
4. How to improve the accuracy of a long read assembly using short reads
5. 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

https://stanford.edu/~yatisht/pubs/darwin-wga.pdf

Address of the bookmark: https://github.com/gsneha26/Darwin-WGA

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
2. Intact ordering and orienting of contigs.
3. Misassembly correction
4. GFF lift-over
5. Structural variant calling with and integrated version of Assemblytics
6. Confidence scores associated with the grouping, localization, and orientation for each contig.

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

https://www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes

Address of the bookmark: https://jimb.stanford.edu/giab/

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake

All genomes in the dataset were sequenced to at least 30x coverage using Illumina technology. The sequencing reads were mapped and genotyped using a customized procedure that was optimized for population genetic analysis. The researchers eliminated bias of alleles toward matching the human genome reference sequence, and determined genotypes on a single-sample basis to avoid preferential calling of genotypes from populations that had more individuals represented.

Address of the bookmark: https://www.simonsfoundation.org/simons-genome-diversity-project/

Please cite:

Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). https://doi.org/10.1038/s41587-019-0201-4

Address of the bookmark: http://daehwankimlab.github.io/hisat2/download/#h-sapiens

Classificier of reads from metagenomic sequencing experiments.

•  Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23,

CoMSA

Compressor of multiple sequence alignments of proteins.

•  Deorowicz, S., Walczyszyn, J., Debudaj-Grabysz, A., CoMSA: compression of protein multiple sequence alignment files, Bioinformatics, 2019; 35(2):22–234,

DSRC

Compressor of sequencing reads.

•  Roguski, L., Deorowicz, S., DSRC 2: Industry-oriented compression of FASTQ files, Bioinformatics, 2014; 30(15):2213–2215,
•  Deorowicz, S., Grabowski, Sz., Compression of DNA sequences in FASTQ format, Bioinformatics, 2011; 27(6):860–862,

FAMSA

Multiple sequence alignment designed for huge families of proteins (even containing hundreds of thousands of sequences).

•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., FAMSA: Fast and accurate multiple sequence alignment of huge protein families, Scientific Reports, 2016; 6(33964):

FaStore

Compressor of FASTQ files.

•  Roguski, L., Ochoa, I., Hernaez, M., Deorowicz, S., FaStore - a space-saving solution for raw sequencing data, Bioinformatics, 2018; 34(16):2748–2756,

FQSqueezer

Experimental high-end compressor of FASTQ files.

•  Deorowicz, S., FQSqueezer: k-mer-based compression of sequencing data, Scientific Reports, 2020; 10(578):

GDC

Compressor of collections of genome sequences.

•  Deorowicz, S., Danek, A., Niemiec, M., GDC 2: Compression of large collections of genomes, Scientific Reports, 2015; 5(11565):1–12,
•  Deorowicz, S., Grabowski, Sz., Robust relative compression of genomes with random access, Bioinformatics, 2011; 27(21):2979–2986,

GTC

Genotype databases compressor with support for fast queries.

•  Danek, A., Deorowicz, S., GTC: how to maintain huge genotype collections in a compressed form, Bioinformatics, 2018; 34(11):1834–1840,

GTShark

Genotypes compressor.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, Bioinformatics, 2019; 35(22):4791–4793,

KMC

Memory frugal k-mer counter.

•  Kokot, M., Długosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759–2761,
•  Deorowicz, S., Kokot, M., Grabowski, Sz., Debudaj-Grabysz, A., KMC 2: Fast and resource-frugal k-mer counting, Bioinformatics, 2015; 31(10):1569–1576,
•  Deorowicz, S., Debudaj-Grabysz, A., Grabowski, Sz., Disk-based k-mer counting on a PC, BMC Bioinformatics, 2013; 14():Article no. 160,

Kmer-db

Tool for estimation of evolutionary distances in a collection of genomes.

•  Deorowicz, S., Gudys, A., Dlugosz, M., Kokot, M., Danek, A., Kmer-db: instant evolutionary distance estimation, Bioinformatics, 2019; 35(1):133–136,

MuGI

Index allowing queries for a collection of multiple genome sequences.

•  Danek, A., Deorowicz, S., Grabowski, Sz., Indexes of Large Genome Collections on a PC, PLOS ONE, 2014; 9(10):e109384,

ORCOM

Experimental compressor of sequencing reads.

•  Grabowski, Sz., Deorowicz, S., Roguski, L., Disk-based compression of data from genome sequencing, Bioinformatics, 2014; 31(9):1389–1395,

PgSA

Index allowing queries for a collection of sequencing reads.

•  Kowalski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE, 2015; 10(7):1–16,

QuickProbs

Multiple sequence alignment designed especially for GPU.

•  Gudys, A., Deorowicz, S., QuickProbs 2: towards rapid construction of high-quality alignments of large protein families, Scientific Reports, 2017; 7(41553):
•  Gudys, A., Deorowicz, S., QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors, PLOS ONE, 2014; 9(2):e88901,

RECKONER

Read error corrector.

•  Maciej Długosz, M., Deorowicz, S., RECKONER: read error corrector based on KMC, Bioinformatics, 2017; 33(7):1086–1089,

TGC

Compressor of collections of genomes given in Variant Call Format (VCF) files.

•  Deorowicz, S., Danek, A., Grabowski, Sz., Genome compression: a novel approach for large collections, Bioinformatics, 2013; 29(20):2572–2578,

VCFShark

Compressor of VCF files.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, biorxiv.org, 2020; ():

Whisper

Experimental mapper of whole genome sequencing data.

•  Deorowicz, S., Gudys, A., Whisper 2: indel-sensitive short read mapping, bioRxiv.org, 2019; :
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Whisper: read sorting allows robust robust mapping of DNA sequencing data, Bioinformatics, 2019; 35(12):2043–2050,
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Robust mapping of whole genome sequencing data, Poster at The Biology of Genomes Conference, 2017;

Address of the bookmark: https://github.com/martinjvickers/KAST

Address of the bookmark: https://github.com/sc932/ALE