FLASH: fast length adjustment of short reads to improve genome assemblies

By Tanja Magoc, Steven L. Salzberg. 2011

13,684 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. M. Miya
2. Q. Shen
3. Henrik Flyvbjerg
4. Fengzhi Wu
5. Xingang Zhou
6. M. Delgado‐Baquerizo
7. T. Sado
8. E. Casamayor

In Genetics

1. Robert C. Edgar
2. M. Delgado‐Baquerizo
3. C. Ruiz‐González
4. Juan Pablo Niño-Garcia
5. Chelsea A. Harms-Tuohy
6. R. Song
7. J. Soininen
8. J. Krause

In Molecular Biology

1. J. Cryan
2. Ted G. Dinan
3. G. Clarke
4. C. Stanton
5. Robert C. Edgar
6. Peer Bork
7. M. Miya
8. Q. Shen

Citations in the corpus

• Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes (2019, methodology): “Microbiome Pipeline Analysis steps—Raw paired-end 16S rRNA reads (V4 region) were merged into consensus fragments by FLASH (Magoc and Salzberg, 2011) and subsequently filtered for quality (targeted error rate 0.5”
• Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico (2016, methodology): “Resulting reads were cleaned in the FASTQ filing and extended using FLASH pair software (Mago & Salzberg 2011).”
• Effects of Two Trichoderma Strains on Plant Growth, Rhizosphere Soil Nutrients, and Fungal Community of Pinus sylvestris var. mongolica Annual Seedlings (2019, methodology): “The sequences were then divided into operational taxonomic units (OTUs) with a 97% similarity cutoff, after which chimeras were removed using UCHIME [40,41].”
• Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation (2016, methodology): “The paired-end FASTQ sequences of original pyrosequencing data were quality-filtered by slip window sampling with the average quality of alkaline bases P20 and sequence length P150 bp; then, FLASH software (version 1.2.7) (Magoč and Salzberg, 2011) was used to link these sequences.”
• Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, methodology): “Reads were pre-quality filtered and trimmed at the 3′-end to 280 bp using PRINSEQ [76] and then merged with FLASH [77].”