Clumpify.sh
WebAny alternatives to BBMap's clumpify.sh program to optimize gzip compression? discussion I've had some difficulties implementing this in pipelines because it randomly fails … WebExample job. Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead. To run bbtools on our clusters: #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bbtools #SBATCH --mail …
Clumpify.sh
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WebMar 31, 2024 · When that is matched to clumpify, you request as input: {AD50_CTGATCGTA_2_val}_2_val_2.fq.gz, which is why you are missing that file. To … WebSo to add some items inside the hash table, we need to have a hash function using the hash index of the given keys, and this has to be calculated using the hash function as …
Webclumpify.sh in=synth_e2_s5.fa.gz out=synth_e2_s5_clumped_s1.fa.gz reorder zl=9 fastawrap=4000 groups=1 dedupe s=1 rcomp # Create baseline kmer sets at different depths for different sensitivites (only one depth is needed) kcompress.sh -Xmx31g ow zl=9 pigz=16 min=1000 in=dd2_e2_s5_masked.fa.gz out=stdout.fa ... WebYou can call dedupe.sh or dedupe2.sh; internally, either Dedupe or Dedupe2 will get used depending on how many affixes were requested with the “nam” (“numaffixmaps”) flag. …
Clumpify supports paired reads, in which case it will clump based on read 1 only. However, it’s much more effective to treat reads as unpaired. For example, merge the reads with BBMerge, then concatenate the merged reads with the unmerged pairs, and clump them all together as unpaired. See more Clumpify stores all sequences in memory while clumping. But it is also capable of operating in two phases, KmerSplit and KmerSort. KmerSplit will break the data up into an arbitrary number of temporary files which can then be … See more Gzip compression is more efficient when similar sequences are nearby, as they can be replaced by pointers to prior copies of that sequence. So, a … See more Webclumpify.sh in=reads.fq.gz out=clumped.fq.gz reorder. This command assumes paired, interleaved reads or single-ended reads. But Clumpify also now works with paired reads …
WebSep 8, 2024 · Quality control included several processes, such as removal of duplicates (with “clumpify.sh”), adapter trimming (using “bbduk.sh”), quality trimming (>Q20), polymer trimming (>10 bp for poly-A/G/C tails), length filtering (>15 bp), and the correction of overlapping paired reads. K-mer analysis was performed by khist.sh with 21 k-mers.
WebContribute to yxu-lanl/nmdc-docs-test development by creating an account on GitHub. crathes cafeWebDescription: Sorts sequences to put similar reads near each other. Can be used for increased compression or error correction. Please read … dj afro apocalyptoWebApr 14, 2024 · Recently Concluded Data & Programmatic Insider Summit March 22 - 25, 2024, Scottsdale Digital OOH Insider Summit February 19 - 22, 2024, La Jolla crathes car show 2022WebDescription: Sorts sequences to put similar reads near each other. This is a wrapper for KmerSplit and KmerSort. Works best with single-ended data. Usage: clumpify.sh … dja dja wurrung corporationWebIdentical PCR optical and tile-edge duplicates for Hi-C reads were removed by the script clumpify.sh from BBTools suite. Assemble shotgun reads For the shotgun library, de novo metagenome assembly is produced by an assembly software, such as MEGAHIT. dj afro fity fityWebclump (klŭmp) n. 1. A clustered mass; a lump: clumps of soil. 2. A thick grouping, as of trees or bushes. 3. A heavy dull sound; a thud. v. clumped, clump·ing, clumps v.intr. 1. To form … crathes castle aberdeenshire christmasWebSynonyms for CLUMPY: lumpy, thick, curdy, chunky, nubbly, nubby, viscous, jagged; Antonyms of CLUMPY: smooth dja dja wurrung clans corporation