{"added":null,"apiVersion":1,"behindSince":null,"buildDepends":[],"categories":["biology"],"comment":"Filter reads from a FASTQ file","compare":null,"dependentCount":null,"description":"Filter reads from a FASTQ file using a list of identifiers.\n\nEach entry in the input FASTQ file (or files) is checked against all\nentries in the identifier list. Matches are included by default, or\nexcluded if the --invert flag is supplied. Paired-end files are kept\nconsistent (in order).\n\nThis is almost certainly not the most efficient way to implement this\nfiltering procedure. I tested a few different strategies and this one\nseemed the fastest. Current timing with 16 processes is about 10\nminutes per 1M paired reads with gzip'd input and output, depending on\nthe length of the identifier list to filter by.\n\nusage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS]\n                       [-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]","flavors":[],"html":"https://daemonports.org/netbsd/biology/filter-fastq/","kind":"port","lastUpdate":null,"license":["mit"],"maintainer":"pkgsrc-users@NetBSD.org","name":"filter-fastq","newest":false,"newestVersion":null,"noVulnData":false,"origin":"biology/filter-fastq","otherSystems":[],"packages":[{"repo":"NetBSD 10.1 x86_64","versions":["0.0.0.20210527nb2"]},{"repo":"NetBSD 10.1 aarch64","versions":["0.0.0.20210527nb2"]},{"repo":"SmartOS / illumos x86_64","versions":["0.0.0.20210527nb2"]},{"repo":"macOS 15 arm64","versions":["0.0.0.20210527nb2"]}],"pkgName":"filter-fastq-0.0.0.20210527nb2","related":null,"repository":"pkgsrc","requiredBy":[],"requiredByCount":0,"runDepends":["lang/python27"],"status":null,"system":"netbsd","systemLabel":"NetBSD","version":"0.0.0.20210527nb2","versions":null,"vulnerabilities":null,"www":"https://github.com/stephenfloor/filter-fastq/"}