Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Hawkins MTR, Hofman CA, Callicrate T, McDonough MM, Tsuchiya MTN, Gutierrez EE, Helgen KM, Maldonado JE

Date Published: July 21, 2015

DOI: http://dx.doi.org/10.5061/dryad.gq883

 

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Title chimera_ID
Description This script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes.
Download chimera_ID.py (2.308 Kb)
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Title combiner-2.0
Description The FASTA file is sequences from MMA capture. The Blast output is the output of blasting those sequences against the MMA probeset, minus closest relative to the target species (non-closest-relative, or NCR, probeset). This program appends the length of the query sequence (found in the FASTA file) onto the end of that sequence's line in the blast table so that the chimera detection decision rules can be followed in chimera_ID.py
Download combiner-2.0.py (2.491 Kb)
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Title sequenceGetter-4.0
Description This script gets a subset of a FASTA file based on a CSV file of BLAST hits.
Download sequenceGetter-4.0.py (2.048 Kb)
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Title AllProbes_good
Description This file contains all 8,178 probes used for RNA bait synthesis.
Download AllProbes_good.fasta (1.119 Mb)
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Title H3FTPWM01
Description 454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run.
Download H3FTPWM01.sff (196.0 Mb)
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Title H3HWW5Q01
Description Second 454 run containing novel mitogenomes. Details for demultiplexing are provided in a separate text file.
Download H3HWW5Q01.sff (155.3 Mb)
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Title WMG_Alignment26Ind_FINAL01.09.14
Description All mitochondrial genomes used for array design. 16 are published sequences and 10 are novel mitogenomes.
Download WMG_Alignment26Ind_FINAL01.09.14.txt (429.9 Kb)
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Title Dryad_ModernSquirrelDemux
Description This file contains the 454 barcode information to demultiplex the samples from the two 454 sff files.
Download Dryad_ModernSquirrelDemux.txt (508 bytes)
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Title pero_in.454.fasta
Description This file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98.
Download pero_in.454.fasta.qual (2.678 Mb)
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Title Enrichment Assemblies
Description These are all 63 assemblies, in bam format with the resulting consensus sequences as fasta. All sequences are labelled by capture pool ID in table 2.
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When using this data, please cite the original publication:

Hawkins MTR, Hofman CA, Callicrate T, McDonough MM, Tsuchiya MTN, Gutierrez EE, Helgen KM, Maldonado JE (2016) In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA. Molecular Ecology Resources 16(5): 1173–1188. http://dx.doi.org/10.1111/1755-0998.12448

Additionally, please cite the Dryad data package:

Hawkins MTR, Hofman CA, Callicrate T, McDonough MM, Tsuchiya MTN, Gutierrez EE, Helgen KM, Maldonado JE (2015) Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gq883
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