Pysamstats

[…] for inconsistencies. to estimate the sequencing depth of each base, bowtie v. 1.0.0 was used to align illumina reads onto the assembled mitogenomes. aligned reads were viewed using igv, tablet, pysamstats (v. 0.84) and bamstats (v. 1.25) [–]. heteroplasmic sites were identified using three conditions: first, different nucleotides were sequenced in the same position; second, that position […]

[…] filtered by quality (q30), and the adapter sequences were removed by trimmomatic. the bowtie 2 tool was used for aligning sequencing reads to references. alignments were processed using samtools and pysamstats software, and figures were generated in the r environment., first, enrichment efficiency was estimated by comparison of the host:viral cdna ratio in libraries […]

[…] standard alignment metrics were generated for each sample using the bamcheck utility from samtools., cnvs spanning the pvmdr1 region (pvx_080100; pv_sal1_chr10:361,701–366 095) were detected using pysamstats (available at: http://github.com/alimanfoo/pysamstats, accessed 15 august 2016). for each sample, coverage in nonoverlapping 300–base pair bins was calculated and normalized by dividing […]

[…] by trimmomatic-0.32 (). a de novo assembly was generated using spades-3.0 (). the reads were then remapped to the assembly with bowtie 2 (). alignments were processed using samtools () and the pysamstats software to estimate genome coverage., overall, the assembly generated three contigs (17,179 nt, 15,473 nt, and 2,048 nt). the median coverage depths were 315×, 95×, and 30×, respectively. […]

[…] on the cellular overview tool of the tb database (tbdb.org) [] we formally tested for an enrichment of genes in this category using a two-sided fisher’s exact test., we used the python package pysamstats (https://github.com/alimanfoo/pysamstats) to calculate the root-mean-square (rms) value of base qualities for variant alleles and the rms mapping quality for reads aligned […]

[…] et al. and available on genbank under accession number kx034166. to search for b-specific sequence variants, we quantified the number of reads carrying a given nucleotide at each position using pysamstats (https://github.com/alimanfoo/pysamstats), and selected the positions where the variants were shared by the two + b libraries but were absent in the two 0b libraries. […]

[…] the assembly against the inferred mitogenome sequence. for this purpose, we used the ssaha2 software [] with a minimum score of 100. then we extracted coverage information from these mapping using pysamstats (available at: http://github.com/alimanfoo/pysamstats)., the mt genomes were annotated using the mitos web server [] applying the invertebrate mitochondrial genetic code and followed […]

[…] for inconsistencies. to estimate the sequencing depth of each base, bowtie v. 1.0.0 was used to align illumina reads onto the assembled mitogenomes. aligned reads were viewed using igv, tablet, pysamstats (v. 0.84) and bamstats (v. 1.25) [–]. heteroplasmic sites were identified using three conditions: first, different nucleotides were sequenced in the same position; second, that position […]

[…] reference with function gatk/printreads in bqsr mode., to detect polymorphisms along the 45s rdna we retrieved per-site information with both the function variation_strand from the python package pysamstats (v0.24.2; a. miles, https://github.com/alimanfoo/pysamstats) and a patched version of it that filters out bases with base quality lower than 20. while we used the output of the former […]

[…] wang, li, & hakonarson, ). finally, the target region reads depth was controlled using bedtools (v.2.25.0; quinlan & hall, ) and the alternative allele frequency was computed using pysamstats (v.0.24.2; https://github.com). candidate variants were filtered according to read depth, allele frequency, and prevalence in genomic variant databases such as exac (v.0.3), clinvar, […]