palfinder

[…] assemblies for both species to assess if ssr content varied among genome assemblies compared to the raw reads (which might indicate the under-representation of ssrs in certain assemblies). we used palfinder v0.02.03 to identify ssrs across genome assemblies, with an ssr being classified as a stretch of 2–6mer tandem repeats that met a certain tandem repeat threshold: 6 tandem repeats […]

[…] than two, mapping quality less than 22, or mapping quality rank sum score less than -20 were filtered out. for indels, only those with quality depth scores less than 2 were filtered out. we used palfinder [], custom perl scripts, and bedtools [] to identify microsatellite loci in the raw sequencing reads and vcf files. a microsatellite locus was considered to be entirely located within […]

[…] (illumina, san diego, california, usa)., the resulting raw illumina paired-end sequencing reads were analyzed with a perl script, pal_finder_v0.02.04 (available at http://sourceforge.net/projects/palfinder), which identifies microsatellite loci without the need for prior sequence trimming and assembly (). the perl script was run with primer3 version 2.0.0 () for simultaneous primer design. […]

[…] paired-end reads with fastqc (). the software fastqmcf was used to trim adapters, cut low quality ends and remove low quality reads and their mate-pair read ()., we executed the perl script palfinder to identify short sequence repeat regions (). the script also calls primer3, version 2.0.0, to identify potential primer pairs that span the repeat region (). the minimum number of repeat […]

[…] thus inexpensive) runs that lead us to suspect that it represents the best available choice for this approach., a variety of software is available to identify microsatellites in ngs datasets (misa, palfinder, msatcommander, qdd), and all of these can effectively process data from 454 and illumina platforms. qdd is an open acess program, and among the most user-friendly and versatile […]

[…] (www.evolutionarygenomics.com and www.snakegenomics.org). the perl script (pal_finder_v0.02.03) used to identify and analyze ssr loci is also freely available at http://sourceforge.net/projects/palfinder/and at the authors' web sites. an accessory script for preparing multiplexed ipe data for input into pal_finder is available at the authors' websites. identified sets of ssr loci, together […]