BSD Ports

biology/fastq-trim 0.1.4 FreeBSD

Lightening fast sequence read trimmer

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
BSD2CLAUSE
Categories
biology
Package size
54.4 KiB, 88.9 KiB installed

Description

Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads prior to analyses such as RNA-Seq. it runs in a fraction of the time required by popular trimmers and uses only a few megabytes of RAM, so it will run almost entirely in cache. The design supports adding any number of alignment functions, so it can be easily adapted to any trimming needs.

In the other systems

The newest version among them is 0.1.4, as upstream numbers it.

SystemPortVersionVulnerabilitiesStatusMaintainerLast update
FreeBSDbiology/fastq-trim0.1.4 newestnone known-[email protected]-
NetBSDbiology/fastq-trim0.1.3none known-[email protected]-
HardenedBSDbiology/fastq-trim0.1.4 newestno data-[email protected]-
GhostBSDbiology/fastq-trim0.1.4 newestno data-[email protected]-

Compare across BSDs

Install

Binary package:

pkg install fastq-trim

From the ports tree:

cd /usr/ports/biology/fastq-trim/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	fastq-trim>0:biology/fastq-trim

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.1.40.1.40.1.20.1.40.1.4
FreeBSD:14:quarterly0.1.40.1.4n/a0.1.40.1.4
FreeBSD:15:latest0.1.40.1.4n/a0.1.40.1.4
FreeBSD:15:quarterly0.1.40.1.4n/an/an/a
FreeBSD:16:latest0.1.40.1.4n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

Dependencies

As this port's Makefile names them.

Build 1

Library 2

The full lists below include those, and their dependencies in turn.

Build dependencies 2
Run dependencies 2

Configuration

No options to configure.

Service scripts
none

Files

Manual pages 68
  • FASTQ_TRIM_ADAPTER1(3)
  • FASTQ_TRIM_ADAPTER1_AE(3)
  • FASTQ_TRIM_ADAPTER2(3)
  • FASTQ_TRIM_ADAPTER2_AE(3)
  • FASTQ_TRIM_ADAPTER_MATCH_FUNCTION(3)
  • FASTQ_TRIM_INFILE1(3)
  • FASTQ_TRIM_INFILE1_AE(3)
  • FASTQ_TRIM_INFILE2(3)
  • FASTQ_TRIM_INFILE2_AE(3)
  • FASTQ_TRIM_INSTREAM1(3)
  • FASTQ_TRIM_INSTREAM1_AE(3)
  • FASTQ_TRIM_INSTREAM2(3)
  • FASTQ_TRIM_INSTREAM2_AE(3)
  • FASTQ_TRIM_MAX_MISMATCH_PERCENT(3)
  • FASTQ_TRIM_MIN_LENGTH(3)
  • FASTQ_TRIM_MIN_MATCH(3)
  • FASTQ_TRIM_MIN_QUAL(3)
  • FASTQ_TRIM_OUTFILE1(3)
  • FASTQ_TRIM_OUTFILE1_AE(3)
  • FASTQ_TRIM_OUTFILE2(3)
  • FASTQ_TRIM_OUTFILE2_AE(3)
  • FASTQ_TRIM_OUTSTREAM1(3)
  • FASTQ_TRIM_OUTSTREAM1_AE(3)
  • FASTQ_TRIM_OUTSTREAM2(3)
  • FASTQ_TRIM_OUTSTREAM2_AE(3)
  • FASTQ_TRIM_PHRED_BASE(3)
  • FASTQ_TRIM_POLYA_MIN_LEN(3)
  • FASTQ_TRIM_VERBOSE(3)
  • fastq-scum(1)
  • fastq-trim(1)
  • fastq_trim_set_adapter1(3)
  • fastq_trim_set_adapter1_ae(3)
  • fastq_trim_set_adapter1_cpy(3)
  • fastq_trim_set_adapter2(3)
  • fastq_trim_set_adapter2_ae(3)
  • fastq_trim_set_adapter2_cpy(3)
  • fastq_trim_set_adapter_match_function(3)
  • fastq_trim_set_infile1(3)
  • fastq_trim_set_infile1_ae(3)
  • fastq_trim_set_infile1_cpy(3)
  • fastq_trim_set_infile2(3)
  • fastq_trim_set_infile2_ae(3)
  • fastq_trim_set_infile2_cpy(3)
  • fastq_trim_set_instream1(3)
  • fastq_trim_set_instream1_ae(3)
  • fastq_trim_set_instream1_cpy(3)
  • fastq_trim_set_instream2(3)
  • fastq_trim_set_instream2_ae(3)
  • fastq_trim_set_instream2_cpy(3)
  • fastq_trim_set_max_mismatch_percent(3)
  • fastq_trim_set_min_length(3)
  • fastq_trim_set_min_match(3)
  • fastq_trim_set_min_qual(3)
  • fastq_trim_set_outfile1(3)
  • fastq_trim_set_outfile1_ae(3)
  • fastq_trim_set_outfile1_cpy(3)
  • fastq_trim_set_outfile2(3)
  • fastq_trim_set_outfile2_ae(3)
  • fastq_trim_set_outfile2_cpy(3)
  • fastq_trim_set_outstream1(3)
  • fastq_trim_set_outstream1_ae(3)
  • fastq_trim_set_outstream1_cpy(3)
  • fastq_trim_set_outstream2(3)
  • fastq_trim_set_outstream2_ae(3)
  • fastq_trim_set_outstream2_cpy(3)
  • fastq_trim_set_phred_base(3)
  • fastq_trim_set_polya_min_len(3)
  • fastq_trim_set_verbose(3)
pkg-plist 75
  • bin/fastq-scum
  • bin/fastq-trim
  • include/fastq-trim-accessors.h
  • include/fastq-trim-mutators.h
  • include/fastq-trim-rvs.h
  • include/fastq-trim.h
  • lib/libfastq-trim.a
  • share/man/man1/fastq-scum.1.gz
  • share/man/man1/fastq-trim.1.gz
  • share/man/man3/FASTQ_TRIM_ADAPTER1.3.gz
  • share/man/man3/FASTQ_TRIM_ADAPTER1_AE.3.gz
  • share/man/man3/FASTQ_TRIM_ADAPTER2.3.gz
  • share/man/man3/FASTQ_TRIM_ADAPTER2_AE.3.gz
  • share/man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3.gz
  • share/man/man3/FASTQ_TRIM_INFILE1.3.gz
  • share/man/man3/FASTQ_TRIM_INFILE1_AE.3.gz
  • share/man/man3/FASTQ_TRIM_INFILE2.3.gz
  • share/man/man3/FASTQ_TRIM_INFILE2_AE.3.gz
  • share/man/man3/FASTQ_TRIM_INSTREAM1.3.gz
  • share/man/man3/FASTQ_TRIM_INSTREAM1_AE.3.gz
  • share/man/man3/FASTQ_TRIM_INSTREAM2.3.gz
  • share/man/man3/FASTQ_TRIM_INSTREAM2_AE.3.gz
  • share/man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3.gz
  • share/man/man3/FASTQ_TRIM_MIN_LENGTH.3.gz
  • share/man/man3/FASTQ_TRIM_MIN_MATCH.3.gz
  • share/man/man3/FASTQ_TRIM_MIN_QUAL.3.gz
  • share/man/man3/FASTQ_TRIM_OUTFILE1.3.gz
  • share/man/man3/FASTQ_TRIM_OUTFILE1_AE.3.gz
  • share/man/man3/FASTQ_TRIM_OUTFILE2.3.gz
  • share/man/man3/FASTQ_TRIM_OUTFILE2_AE.3.gz
  • share/man/man3/FASTQ_TRIM_OUTSTREAM1.3.gz
  • share/man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3.gz
  • share/man/man3/FASTQ_TRIM_OUTSTREAM2.3.gz
  • share/man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3.gz
  • share/man/man3/FASTQ_TRIM_PHRED_BASE.3.gz
  • share/man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3.gz
  • share/man/man3/FASTQ_TRIM_VERBOSE.3.gz
  • share/man/man3/fastq_trim_set_adapter1.3.gz
  • share/man/man3/fastq_trim_set_adapter1_ae.3.gz
  • share/man/man3/fastq_trim_set_adapter1_cpy.3.gz
  • share/man/man3/fastq_trim_set_adapter2.3.gz
  • share/man/man3/fastq_trim_set_adapter2_ae.3.gz
  • share/man/man3/fastq_trim_set_adapter2_cpy.3.gz
  • share/man/man3/fastq_trim_set_adapter_match_function.3.gz
  • share/man/man3/fastq_trim_set_infile1.3.gz
  • share/man/man3/fastq_trim_set_infile1_ae.3.gz
  • share/man/man3/fastq_trim_set_infile1_cpy.3.gz
  • share/man/man3/fastq_trim_set_infile2.3.gz
  • share/man/man3/fastq_trim_set_infile2_ae.3.gz
  • share/man/man3/fastq_trim_set_infile2_cpy.3.gz
  • share/man/man3/fastq_trim_set_instream1.3.gz
  • share/man/man3/fastq_trim_set_instream1_ae.3.gz
  • share/man/man3/fastq_trim_set_instream1_cpy.3.gz
  • share/man/man3/fastq_trim_set_instream2.3.gz
  • share/man/man3/fastq_trim_set_instream2_ae.3.gz
  • share/man/man3/fastq_trim_set_instream2_cpy.3.gz
  • share/man/man3/fastq_trim_set_max_mismatch_percent.3.gz
  • share/man/man3/fastq_trim_set_min_length.3.gz
  • share/man/man3/fastq_trim_set_min_match.3.gz
  • share/man/man3/fastq_trim_set_min_qual.3.gz
  • share/man/man3/fastq_trim_set_outfile1.3.gz
  • share/man/man3/fastq_trim_set_outfile1_ae.3.gz
  • share/man/man3/fastq_trim_set_outfile1_cpy.3.gz
  • share/man/man3/fastq_trim_set_outfile2.3.gz
  • share/man/man3/fastq_trim_set_outfile2_ae.3.gz
  • share/man/man3/fastq_trim_set_outfile2_cpy.3.gz
  • share/man/man3/fastq_trim_set_outstream1.3.gz
  • share/man/man3/fastq_trim_set_outstream1_ae.3.gz
  • share/man/man3/fastq_trim_set_outstream1_cpy.3.gz
  • share/man/man3/fastq_trim_set_outstream2.3.gz
  • share/man/man3/fastq_trim_set_outstream2_ae.3.gz
  • share/man/man3/fastq_trim_set_outstream2_cpy.3.gz
  • share/man/man3/fastq_trim_set_phred_base.3.gz
  • share/man/man3/fastq_trim_set_polya_min_len.3.gz
  • share/man/man3/fastq_trim_set_verbose.3.gz
distinfo 1
FileSizeSHA256
outpaddling-fastq-trim-0.1.4_GH0.tar.gz29825e31cdccdf0e68f68142917fffaceb9e814b3f217382c2e0f3663a6e1c7a13bb6

Commit history 0

No commits in the history this site was built from.