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bioawk specifications

Information


Unique identifier OMICS_11293
Name bioawk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED, GFF, SAM, VCF, FASTA, FASTQ, TAB
Output format FASTA, SAM
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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bioawk citations

 (4)
library_books

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light Associated Genes

2017
Genome Biol Evol
PMCID: 5629816
PMID: 28992302
DOI: 10.1093/gbe/evx158

[…] ing 16,500 nt, the approximate size of the mitochondrial genomes of other owl (Aves: Strigiformes) species (; ; ; ). We extracted the scaffold corresponding to the mitochondrial genome assembly using bioawk version 1.0 () and annotated it using the MITOS WebServer version 806 () (supplementary section 1.21, online). We will refer to the mitochondrial and nuclear genome assemblies hereafter as Str […]

library_books

Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

2017
PeerJ
PMCID: 5639871
PMID: 29038757
DOI: 10.7717/peerj.3901

[…] gallus (GenBank Accessions NC_001323 () and AB086102.1 ()) in Geneious version 9.1.4. We annotated the repetitive regions using the web version of Tandem Repeats Finder version 4.09 (; ) (). We used bioawk version 1.0 () and GAWK version 4.0.1 to find goose hairpin sequences in CR1 and CR2 (). We compared the sequences of the annotated genes in our final mitochondrial genome assembly with those o […]

library_books

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn's disease

2016
Nat Commun
PMCID: 5122959
PMID: 27876802
DOI: 10.1038/ncomms13419

[…] tq format and reads split according to the expected sizes for the V4/V6 regions plus the barcodes (234–266 and 162–194, respectively, representing a ±16 bp window), using samtools in conjunction with bioawk (https://github.com/lh3/bioawk). The reads were quality trimmed using the modified Mott trimming algorithm implemented in seqtk (https://github.com/lh3/seqtk) and reads that were shorter than t […]

call_split

Complete Mitochondrial Genomes of New Zealand’s First Dogs

2015
PLoS One
PMCID: 4596854
PMID: 26444283
DOI: 10.1371/journal.pone.0138536
call_split See protocol

[…] analysed only 16,195 bp of the mitochondrial genome to allow them to exclude repetitive and difficult-to-align regions. The control region (15458–16039) was extracted from Wairau Bar sequences using bioawk (https://github.com/lh3/bioawk) for comparison with the modern control region haplotypes.Median joining networks were then created with these datasets. In addition, the ancient Polynesian short […]

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