Back

ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs.

Wegner, M.; Kaulich, M.

2023-03-10 bioinformatics
10.1101/2023.03.09.530923 bioRxiv
Show abstract

SummaryCRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 for rapid sequence trimming and alignment, ReCo enables the automated generation of read count tables from staggered NGS reads for the downstream identification of gRNA-induced phenotypes. Availability and implementationReCo is published under the MIT license and available at: https://github.com/KaulichLab/ReCo. Supplementary informationSupplementary data are available at Bioinformatics online.

Matching journals

The top 2 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.2%
46.1%
Similar papers in this journal
2
BMC Bioinformatics
○ 457 papers in training set
Top 0.7%
9.8%
Similar papers in this journal
50% of probability mass above
3
Bioinformatics Advances
◐ 203 papers in training set
Top 0.4%
8.0%
Similar papers in this journal
4
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 1%
3.3%
Similar papers in this journal
5
Nucleic Acids Research
◐ 1281 papers in training set
Top 5%
3.3%
Similar papers in this journal
6
GigaScience
◐ 212 papers in training set
Top 1%
2.7%
7
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.1%
8
BMC Genomics
○ 406 papers in training set
Top 4%
1.7%
9
Life Science Alliance
● 285 papers in training set
Top 4%
1.4%
10
PLOS Computational Biology
● 1863 papers in training set
Top 16%
1.3%
11
The CRISPR Journal
○ 39 papers in training set
Top 0.3%
1.1%
12
Molecular Ecology Resources
○ 171 papers in training set
Top 2%
1.1%
13
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 4%
1.1%
14
Genome Research
● 468 papers in training set
Top 5%
1.1%
15
Frontiers in Genetics
○ 230 papers in training set
Top 4%
1.0%
16
Genome Biology
○ 637 papers in training set
Top 8%
1.0%
17
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 4%
0.9%
18
PeerJ
◐ 308 papers in training set
Top 10%
0.9%
19
Scientific Reports
○ 3612 papers in training set
Top 71%
0.9%
20
F1000Research
○ 88 papers in training set
Top 4%
0.9%
21
Nature Communications
○ 5641 papers in training set
Top 58%
0.6%
22
Methods in Ecology and Evolution
○ 176 papers in training set
Top 2%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.