Aligning short sequencing reads with Bowtie

By Ben Langmead. Current Protocols in Bioinformatics, 2010

1,288 citations recorded by the source corpus.

This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools. Curr. Protoc. Bioinform. 32:11.7.1‐11.7.14. © 2010 by John Wiley & Sons, Inc.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/1045e6fd708ca28c088eee90a8837f98b1ca29af

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Citations in the corpus

LINE-1 derepression in senescent cells triggers interferon and inflammaging (2019, positive): “Transcription factor ChIP-seq and input control reads were aligned to the consensus sequence of L1HS using bowtie1 48 .”
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades (2011, methodology): “Then the processed reads are mapped against the reference genome with the Bowtie tool (34).”
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments (2012, neutral): “Then, all the unique reads are aligned to the corresponding reference sequences by Bowtie [31] in”
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition (2014, methodology): “0] using Bowtie (Langmead, 2010) with the command-line options ‘-q −5 5 -3 5 -l 70 -n 2 -a -m 1 –best strata’, thereby trimming 5 bases from each end of the 100 base single reads, and keeping only tags that mapped uniquely to the genomes with at most two mismatches.”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, neutral): “Thus, comparative genomics has turned to highly efficient and accurate read mapping algorithms to carry out assembly-free analyses, spawning many mapping tools [49-52] and variant callers [53-55] for detecting SNPs and short Indels.”