Correction to: IonCRAM: a reference-based compression tool for ion torrent sequence files
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2020) 21:435
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CORRECTION
Correction to: IonCRAM: a reference‑based compression tool for ion torrent sequence files Moustafa Shokrof1 and Mohamed Abouelhoda2,3,4*
The original article can be found online at https://doi. org/10.1186/s12859-02003726-9. *Correspondence: [email protected] 4 Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, University Square, Giza, Egypt Full list of author information is available at the end of the article
Correction to: BMC Bioinformatics (2020) 21:397 https://doi.org/10.1186/s12859-020-03726-9 Following publication of the original article [1], the authors identified a missing section in the published article. The missing section is given below. Algorithm IonCRAM-CompressBAM 1 Sort the BAM file (if not sorted) by genomic coordinates. Then sort the reads starting at the same locus lexicographically via sorting their CIGAR string. 2 Separate the signals of the forward reads from those of the reverse ones and process each group independently (in parallel) using Steps 3 and 4. 3 Remove the flow signals from the BAM file and store them separately. Compress the remaining fields of the BAM file (sequence, quality, and other fields) using a reference based method (We use the program Scramble [20] for this step.) 4 Define blocks of flow signals, such that the reads in each block are mapped to the same locus. Each block B can be processed in parallel using the steps 4.1 to 4.3: 4.1 Let Fr denote the rth flow-signal vector in B (r ∈ [1..m]), and let Fr[i] ∈ ℤ denote the ith component of it, 1 ≤ i ≤ n. Take F1 as a reference vector and compute the difference vector Dj, where Dj[i] = Fj[i] – Fj+1 [i], 1 ≤ i ≤ n, 1 ≤ j 255 for any x, then we write 255 in Vj1[x] and write the values (Dj[x]-255) in a separate list Vj2. (The length of Vj2 list equals the number of values larger than 255 in Dj and they are very rare in practice.) 6.1 Concatenate F1 and the V vectors and compress them. (We use the XZ algorithm as default method for that purpose.) (F1 is a reference flow signal vector that will be used in decompression). 5 Wait until all (parallel) processes finish. Use the Linux tar package to create a compressed folder including the compressed B blocks files and the other compressed CRAM files computed in Step 1.
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