From 9fbf2ee4b25ba536d121b5d9db0bb264ff3e3ce9 Mon Sep 17 00:00:00 2001 From: guilhermesena1 Date: Tue, 3 Aug 2021 11:44:13 -0700 Subject: [PATCH] updating README.md (abismal capitalization and user flags) --- README.md | 60 +++++++++++++++++++++++++++++-------------------------- 1 file changed, 32 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index e0ba8d4..2f07049 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,24 @@ -## ABISMAL ## +## abismal ## -**A**nother **Bis**ulfite **M**apping **Al**gorithm (ABISMAL) is +**A**nother **Bis**ulfite **M**apping **Al**gorithm (abismal) is a read mapping program for bisulfite sequencing in DNA methylation studies. ### Requirements ### -Currently ABISMAL requires a C++ compiler that supports the C++11 +Currently abismal requires a C++ compiler that supports the C++11 standard and OpenMP. The default compiler assumed is g++ (comes with GCC, available on your Linux or OS X machine). The g++ compiler has supported the C++11 standard since roughly 2012 (GCC 4.7) so this should not cause any problems. It also requires an OMP library and -headers to be available, which rarely causes problems. ABISMAL also is +headers to be available, which rarely causes problems. abismal also is capable of reading input files (FASTQ format) that are gzip compressed. This requires that the ZLib library is installed on the system; this is also rarely a problem. If you have trouble with the `make` part of the installation procedure -described below, please contact me. +described below, please contact us via e-mail or through a [GitHub +issue](https://github.com/smithlabcode/abismal/issues). ### Installation from a clone of the repo ### @@ -68,25 +69,26 @@ paired-end reads $ abismal [options] -i -o ``` -### ABISMAL Options ### - -|option|long version |arg type |default|description | -|:-----|:------------|:--------|------:|:--------------------------------------------------| -| -i | -index | string | | genome index file [required] | -| -o | -outfile | string | stdout | output SAM file | -| -t | -threads | integer | 1 | number of mapping threads | -| -b | -batch | integer | 20,000 | number of reads to load at once | -| -c | -candidates | integer | 0 (automatic) | maximum candidates for comparison | -| -p | -max-mates | integer | 20 | max number of candidates for mating | -| -l | -min-frag | integer | 32 | minimum fragment length (PE mode) | -| -L | -max-frag | integer | 3,000 | maximum fragment length (PE mode) | -| -M | -max-error | double | 0.1 | max relative number of errors | -| -s | -mapstats | string | | mapping statistics output file | -| -a | -ambig | | | report a position for ambiguous reads | -| -P | -pbat | | | input follows the PBAT protocol | -| -R | -random-pbat| | | input follows the random PBAT protocol| -| -A | -a-rich | | | reads are A-rich (SE mode) | -| -V | -verbose | | | print more run info | +### abismal options ### + +|option|long version |arg type |default |description | +|:-----|:--------------|:--------|------------------:|:--------------------------------------| +| -i | -index | string | | genome index file | +| -g | -genome | string | | genome file (FASTA) | +| -o | -outfile | string | stdout | output file (SAM) | +| -t | -threads | integer | 1 | number of mapping threads | +| -b | -batch | integer | 20,000 | number of reads to load at once | +| -c | -candidates | integer | 0 (automatic) | maximum candidates for comparison | +| -p | -max-mates | integer | 20 | max number of candidates for mating | +| -l | -min-frag | integer | 32 | minimum fragment length (PE mode) | +| -L | -max-frag | integer | 3,000 | maximum fragment length (PE mode) | +| -m | -max-distance | double | 0.1 | max relative number of errors | +| -s | -stats | string | | mapping statistics output file (YAML) | +| -a | -ambig | | | report a position for ambiguous reads | +| -P | -pbat | | | input follows the PBAT protocol | +| -R | -random-pbat | | | input follows the random PBAT protocol| +| -A | -a-rich | | | reads are A-rich (SE mode) | +| -V | -verbose | | | print more run info | ### Examples ### @@ -120,14 +122,16 @@ $ abismal -g hg38.fa -o reads.sam reads.fq Mapping results are reported in SAM format. Some choices in the output are explicitly highlighted below: * Reads are output identically to how they were read, regardless of - mapped strand + mapped strand. * the `NM` tag reports the edit distance between the read and the output, specifically the sum of mismatches, insertions and deletions to the best mapping position. * The `CV` tag reports the assumed bisulfite base used to map the read. Reads mapped as A-rich will be reported with `CV:A:A`, and reads mapped as T-rich will be reported with `CV:A:T`. This tag is - independent of the strand the read was mapped to. + independent of the strand the read was mapped to. If reads are not + mapped in PBAT or random PBAT mode, the first end will always be + T-rich and the second end will always be A-rich. ### Contacts ### @@ -140,12 +144,12 @@ Copyright (C) 2018-2021 Andrew D. Smith and Guilherme de Sena Brandine Authors: Andrew D. Smith and Guilherme de Sena Brandine -ABISMAL is free software: you can redistribute it and/or modify it under +abismal is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -ABISMAL is distributed in the hope that it will be useful, but WITHOUT +abismal is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.